Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0007031 peroxisome organization	IBA GO_REF:0000033	ACCEPT	Summary: PEX16 is one of three early peroxins (PEX3, PEX16, PEX19) required for peroxisome membrane biogenesis in mammals. Loss of PEX16 leads to complete absence of peroxisomes. Peroxisome organization is a well-supported core function, though the more specific term peroxisome membrane biogenesis (GO:0016557) better captures PEX16's primary role. This IBA annotation at the broader level is appropriate and phylogenetically sound. Reason: IBA annotations undergo extensive phylogenetic review and this term accurately captures PEX16's role at the appropriate general level. PEX16 is essential for peroxisome organization as demonstrated by the complete loss of peroxisomes in PEX16-deficient cells (PMID:9837814, PMID:9922452, PMID:16717127). Supporting Evidence: PMID:9837814 HsPEX16 expression morphologically and biochemically restored peroxisome biogenesis only in fibroblasts from a CG-D patient with ZS PMID:9922452 expression of PEX16 restores the formation of new peroxisomes in PBD061 cells
GO:0005778 peroxisomal membrane	IBA GO_REF:0000033	ACCEPT	Summary: PEX16 is an integral peroxisomal membrane protein with two transmembrane helices. Both N- and C-terminal domains are exposed to the cytosol. Peroxisomal membrane localization is well established by immunofluorescence, cell fractionation, and topology studies. Reason: Peroxisomal membrane is the primary functional localization of PEX16, confirmed by multiple studies including topology determination (PMID:12223482), immunofluorescence (PMID:9837814), and cell fractionation (PMID:9922452). IBA annotation is phylogenetically appropriate. Supporting Evidence: PMID:12223482 we have determined the membrane topology of Pex16p by differential permeabilization method: both N- and C-terminal parts are exposed to the cytosol PMID:9837814 Pex16p was localized to peroxisomes through expression study of epitope-tagged Pex16p
GO:0005778 peroxisomal membrane	IEA GO_REF:0000120	ACCEPT	Summary: Combined automated annotation for peroxisomal membrane. Consistent with extensive experimental evidence and IBA annotation for the same term. Reason: Redundant with experimentally supported annotations but correct. PEX16 is an integral peroxisomal membrane protein.
GO:0007031 peroxisome organization	IEA GO_REF:0000043	ACCEPT	Summary: IEA annotation based on UniProt keyword mapping for peroxisome organization. Consistent with IBA and experimental annotations for the same term. Reason: Correct and consistent with extensive experimental evidence. PEX16 is essential for peroxisome organization.
GO:0005778 peroxisomal membrane	TAS Reactome:R-HSA-9603775	ACCEPT	Summary: Reactome annotation for peroxisomal membrane localization in the context of PEX3:PEX19:class I PMP dissociation. PEX16 is located at the peroxisomal membrane where PEX3-PEX19-PMP complexes dock. Reason: Correct localization. PEX16 functions at the peroxisomal membrane as the receptor for PEX3-PEX19 complexes (PMID:19114594).
GO:0005778 peroxisomal membrane	TAS Reactome:R-NUL-9604086	ACCEPT	Summary: Reactome annotation for peroxisomal membrane in the context of PEX19:Pex3 binding PEX16. PEX16 serves as the membrane-anchored receptor at the peroxisomal membrane. Reason: Correct localization in context of the PEX3-PEX16 interaction at the peroxisomal membrane (PMID:19114594).
GO:0005778 peroxisomal membrane	TAS Reactome:R-NUL-9604116	ACCEPT	Summary: Reactome annotation for peroxisomal membrane in the context of PEX16:PEX19:Pex3 dissociation. Reason: Correct localization. Multiple Reactome entries for the same CC term are acceptable as they represent different reaction contexts.
GO:0005829 cytosol	TAS Reactome:R-HSA-9603775	REMOVE	Summary: Reactome annotation placing PEX16 in the cytosol. However, PEX16 is an integral membrane protein that is never found in the cytosol. Cell fractionation shows PEX16 resides only in the membrane fraction (PMID:16717127). This Reactome annotation likely refers to the cytosolic face of PEX16 (both N- and C-termini are cytosolic) or to other participants in the reaction, not to PEX16 itself being a cytosolic protein. Reason: PEX16 is an integral membrane protein. Kim et al. (2006) showed by cell fractionation that PEX16-GFP resided only in the membrane (nonsoluble fraction). PEX16 is never cytosolic. This annotation is incorrect for PEX16. Supporting Evidence: PMID:16717127 Cell fractionation and immunoblot analysis of PEX16-GFP-transformed COS-7 cells performed 24 h after transfection to allow for protein overexpression revealed that PEX16-GFP resided only in the membrane (or nonsoluble fraction), in contrast to GFP expressed alone, which was primarily in the soluble fraction
GO:0005829 cytosol	TAS Reactome:R-HSA-9603784	REMOVE	Summary: Reactome annotation placing PEX16 in cytosol for the PEX19:class I PMP binds PEX3 reaction. PEX16 is an integral membrane protein and is not cytosolic. Reason: PEX16 is never found in the cytosol. It is an integral membrane protein localized to peroxisomal membrane and ER membrane (PMID:16717127, PMID:12223482).
GO:0005829 cytosol	TAS Reactome:R-HSA-9603804	REMOVE	Summary: Reactome annotation placing PEX16 in cytosol for the PEX19 binds class I PMPs reaction. PEX16 is an integral membrane protein and is not cytosolic. Reason: PEX16 is never found in the cytosol. It is a multi-pass integral membrane protein (PMID:12223482, PMID:16717127). This Reactome-derived annotation is erroneous for PEX16.
GO:0106101 ER-dependent peroxisome localization	IDA PMID:19479899 Pex3p-dependent peroxisomal biogenesis initiates in the endo...	ACCEPT	Summary: Toro et al. (2009) showed that Pex3p requires Pex16p for ER location and that Pex3p-dependent peroxisomal biogenesis initiates in the ER. Cross-expression experiments demonstrated that Pex3p requires Pex16p for ER location. This annotation captures PEX16's role in ER-dependent peroxisome localization. Reason: Direct evidence from cross-expression experiments showing PEX16's role in ER-dependent peroxisome biogenesis. PEX16 localizes to the ER and recruits other PMPs there for subsequent transport to peroxisomes. Supporting Evidence: PMID:19479899 Cross-expression experiments of Pex3p in GM623 cells lacking Pex16p or Pex16p in MR cells lacking Pex3p, showed evidence that Pex3p requires Pex16p for ER location but is dispensable for the ER location of Pex16p
GO:0016020 membrane	HDA PMID:19946888 Defining the membrane proteome of NK cells.	ACCEPT	Summary: High-throughput mass spectrometry study of NK cell membrane proteome identified PEX16 in the membrane fraction. The term 'membrane' is very generic; PEX16 is specifically localized to peroxisomal membrane and ER membrane. Reason: While very generic, this HDA annotation from a proteomics study is not incorrect -- PEX16 is indeed a membrane protein. More specific terms (peroxisomal membrane, ER membrane) are already annotated. This broad term from a large-scale study is acceptable as supporting evidence.
GO:0005515 protein binding	IPI PMID:19114594 The peroxisomal membrane protein import receptor Pex3p is di...	MODIFY	Summary: Matsuzaki and Fujiki (2008) demonstrated that PEX16 functions as the membrane receptor for PEX3-PEX19 complexes. PEX16 directly binds to PEX3 (shown by co-immunoprecipitation of cell-free synthesized proteins) and serves as the docking site for PEX3-PEX19 complexes at the peroxisomal membrane. The term 'protein binding' is uninformative; a more specific molecular function term should be used. Reason: While the physical interaction between PEX16 and PEX3 is well established, the generic 'protein binding' term is uninformative. PEX16's molecular function is better described as acting as a receptor/docking site for PEX3 in the context of peroxisome membrane biogenesis. A term like 'protein-membrane targeting activity' or 'peroxisomal membrane protein receptor activity' would be more appropriate, but no such specific MF term currently exists in GO. The best available alternative would be to annotate with GO:0022615 (protein to membrane docking) which is already annotated from the same paper. Proposed replacements: protein to membrane docking Supporting Evidence: PMID:19114594 we demonstrate that Pex16p functions as the Pex3p-docking site and serves as the peroxisomal membrane receptor that is specific to the Pex3p-Pex19p complexes
GO:0022615 protein to membrane docking	IDA PMID:19114594 The peroxisomal membrane protein import receptor Pex3p is di...	ACCEPT	Summary: Matsuzaki and Fujiki (2008) showed using semi-intact cell import assays and co-immunoprecipitation that PEX16 functions as the membrane receptor for PEX3-PEX19 complexes. Ectopic expression of EGFP-Pex16p specifically enhanced targeting of Pex3p to peroxisomes 5-6 fold. Knockdown of Pex16p abrogated Pex3p targeting. This term captures PEX16's core molecular function of docking PEX3 at the peroxisomal membrane. Reason: This is a core molecular function annotation for PEX16. The paper provides strong direct evidence that PEX16 serves as the membrane docking receptor for PEX3-PEX19 complexes through in vitro import assays, co-IP, and siRNA knockdown experiments. Supporting Evidence: PMID:19114594 Pex16p functions as a membrane receptor for Pex3p-Pex19p complexes PMID:19114594 thereby indicating that Pex16p functions as a receptor for cytosolic Pex3p-Pex19p complexes PMID:19114594 Pex16p was a prerequisite for peroxisomal targeting of newly synthesized Pex3p in vivo, functioning as the Pex3p membrane receptor
GO:0005777 peroxisome	IDA PMID:21768384 Sec16B is involved in the endoplasmic reticulum export of th...	ACCEPT	Summary: Yonekawa et al. (2011) showed PEX16-GFP localizes to peroxisomes and that Sec16B regulates the ER-to-peroxisome transport of PEX16. The more specific term peroxisomal membrane (GO:0005778) is already annotated with stronger evidence. Reason: Peroxisome localization is correct. While the more specific peroxisomal membrane term is preferred and already annotated, this annotation is not wrong. Supporting Evidence: PMID:21768384 peroxisomal membrane biogenesis factors peroxin 3 (Pex3) and Pex16 were redistributed from peroxisomes to Sec16B-positive ER membranes
GO:0005783 endoplasmic reticulum	IDA PMID:21768384 Sec16B is involved in the endoplasmic reticulum export of th...	ACCEPT	Summary: Yonekawa et al. (2011) demonstrated that PEX16 transits through the ER en route to peroxisomes. Knockdown of Sec16B caused redistribution of PEX16-GFP to the ER, and overexpression of Sec16B also caused PEX16 redistribution to ER membranes. PEX16 ER localization is an intermediate in its trafficking pathway. Reason: PEX16 is found at the ER as an intermediate during its biogenesis and trafficking. This is well established by multiple studies. Supporting Evidence: PMID:21768384 Knockdown of Sec16B but not Sec16A by RNAi affected the morphology of peroxisomes, inhibited the transport of Pex16 from the ER to peroxisomes
GO:0005515 protein binding	IPI PMID:14709540 PEX19 is a predominantly cytosolic chaperone and import rece...	MODIFY	Summary: Jones et al. (2004) showed PEX19 binds to mPTS regions of PEX16 (amino acids 221-336 and 59-219). PEX19 functions as a chaperone and import receptor for class 1 PMPs including PEX16. The interaction is specific and functionally relevant, as PEX19 controls subcellular distribution of PEX16 mPTS-containing fragments. However, 'protein binding' is uninformative. Reason: The PEX19-PEX16 interaction is real and functionally important, but 'protein binding' is uninformative. PEX16 is itself a class 1 PMP that is chaperoned and imported by PEX19. The interaction represents PEX16 being a cargo/substrate of PEX19, not a specific molecular function of PEX16 itself. Since there is no good GO MF term for 'being a substrate of a chaperone', this annotation should be removed in favor of the existing BP annotations that capture the functional context. Proposed replacements: protein import into peroxisome membrane Supporting Evidence: PMID:14709540 PEX19 binds multiple PMP targeting signals PMID:14709540 Both PMP34aa244-307/3xmyc and PEX16aa221-336/3xmyc were imported into peroxisomes in the majority of control cells (88% and 91%, respectively)
GO:0005778 peroxisomal membrane	HDA PMID:21525035 PEX14 is required for microtubule-based peroxisome motility ...	ACCEPT	Summary: Bharti et al. (2011) established a procedure for isolating native peroxisomal membrane protein complexes from human cells and identified PEX14-associated proteins by mass spectrometry. PEX16 was identified as a constituent of peroxisomal membrane complexes, confirming its peroxisomal membrane localization. Reason: High-throughput proteomic identification of PEX16 in peroxisomal membrane complexes is consistent with extensive experimental evidence for peroxisomal membrane localization. Supporting Evidence: PMID:21525035 Using mass spectrometric analysis, almost all known human peroxins involved in protein import were identified as constituents of the PEX14 complexes
GO:0007031 peroxisome organization	IMP PMID:19479899 Pex3p-dependent peroxisomal biogenesis initiates in the endo...	ACCEPT	Summary: Toro et al. (2009) showed using cross-expression experiments in Zellweger syndrome cell lines that PEX16 is required for peroxisome biogenesis. Pex3p requires Pex16p for ER location during de novo peroxisome formation. Reason: Direct mutant phenotype evidence demonstrates PEX16 is required for peroxisome organization. PEX16 is essential for de novo peroxisome biogenesis from the ER. Supporting Evidence: PMID:19479899 Cross-expression experiments of Pex3p in GM623 cells lacking Pex16p or Pex16p in MR cells lacking Pex3p, showed evidence that Pex3p requires Pex16p for ER location but is dispensable for the ER location of Pex16p
GO:0005783 endoplasmic reticulum	IDA PMID:19479899 Pex3p-dependent peroxisomal biogenesis initiates in the endo...	ACCEPT	Summary: Toro et al. (2009) showed that PEX16 localizes to the ER when expressed in ZS cells lacking PEX3 (MR cells), confirming that PEX16 targets the ER independently of PEX3. Reason: ER localization of PEX16 is established as an intermediate in its trafficking pathway, particularly during de novo peroxisome formation. PEX16 targets the ER independently of PEX3. Supporting Evidence: PMID:19479899 Pex3p requires Pex16p for ER location but is dispensable for the ER location of Pex16p
GO:0032581 ER-dependent peroxisome organization	IDA PMID:16717127 The origin and maintenance of mammalian peroxisomes involves...	ACCEPT	Summary: Kim et al. (2006) provided the first direct evidence in mammalian cells that the ER plays a central role in peroxisome biogenesis. They showed PEX16 is cotranslationally inserted into the ER and recruits other PMPs to ER membranes, driving de novo peroxisome formation. PEX16-GFP with an appended signal anchor sequence could complement PEX16-deficient cells, proving the ER pathway is sufficient. Reason: This is a core function annotation. Kim et al. (2006) provided landmark evidence that PEX16 regulates ER-dependent peroxisome formation, recruiting PMPs including PEX3 and PMP34 to ER membranes for subsequent transport to peroxisomes. Supporting Evidence: PMID:16717127 We provide direct evidence that peroxisomes can arise de novo from the ER in both normal and peroxisome-less mutant cells. We further show that PEX16 regulates this process by being cotranslationally inserted into the ER and serving to recruit other peroxisomal membrane proteins to membranes. PMID:16717127 when PEX16-Venus was coexpressed with either PEX3- or PMP34-Cerulean, both PMPs colocalized with PEX16-Venus in the ER
GO:0005777 peroxisome	IDA PMID:9837814 Mutation in PEX16 is causal in the peroxisome-deficient Zell...	ACCEPT	Summary: Honsho et al. (1998) showed Pex16p localized to peroxisomes using epitope-tagged expression studies. This was the original identification of human PEX16. Reason: Original characterization of human PEX16 showing peroxisomal localization. Well supported by subsequent studies. Supporting Evidence: PMID:9837814 Pex16p was localized to peroxisomes through expression study of epitope-tagged Pex16p
GO:0006625 protein targeting to peroxisome	IMP PMID:9837814 Mutation in PEX16 is causal in the peroxisome-deficient Zell...	ACCEPT	Summary: Honsho et al. (1998) showed that PEX16 expression restored peroxisome biogenesis in CG-D patient fibroblasts. This encompasses the targeting of peroxisomal proteins to the newly formed organelle. While PEX16 is more specifically involved in PMP targeting (membrane protein targeting rather than matrix protein targeting), the broader term is not incorrect since PEX16 function is prerequisite for all peroxisomal protein targeting. Reason: PEX16 is required for peroxisome membrane assembly, which is prerequisite for all peroxisomal protein targeting. While PEX16 directly mediates PMP import rather than matrix protein import, loss of PEX16 abolishes all protein targeting to peroxisomes because no peroxisomes exist. Supporting Evidence: PMID:9837814 HsPEX16 expression morphologically and biochemically restored peroxisome biogenesis only in fibroblasts from a CG-D patient with ZS
GO:0016557 peroxisome membrane biogenesis	IMP PMID:9837814 Mutation in PEX16 is causal in the peroxisome-deficient Zell...	ACCEPT	Summary: Honsho et al. (1998) demonstrated that mutation in PEX16 causes loss of peroxisomes in CG-D/CG-IX Zellweger syndrome. Introduction of wild-type PEX16 restores peroxisome biogenesis. This is the most specific and accurate core function annotation for PEX16. Reason: Peroxisome membrane biogenesis is the primary biological process function of PEX16. Patient cells with PEX16 mutations completely lack peroxisomal membranes, and complementation restores them. Supporting Evidence: PMID:9837814 HsPEX16 expression morphologically and biochemically restored peroxisome biogenesis only in fibroblasts from a CG-D patient with ZS
GO:0005515 protein binding	IPI PMID:15713480 Analysis of human Pex19p's domain structure by pentapeptide ...	MODIFY	Summary: Fransen et al. (2005) performed pentapeptide scanning mutagenesis of PEX19 and identified that PEX19's carboxy-terminal domain interacts with multiple PMPs including PEX16. This paper is primarily about PEX19's domain structure, and PEX16 is one of many PMPs tested as a binding partner. The 'protein binding' annotation is uninformative. Reason: Generic protein binding is uninformative. The interaction documented is PEX19 binding PEX16 as a cargo/substrate for chaperoning and import. This is the same interaction documented in PMID:14709540. Should be replaced with a more specific annotation or removed as redundant. Proposed replacements: protein import into peroxisome membrane Supporting Evidence: PMID:15713480 a carboxy-terminal domain that interacts with multiple PMPs including Pex3p, Pex11pbeta, Pex12p, Pex13p, Pex16p, and Pex26p
GO:0005789 endoplasmic reticulum membrane	IDA PMID:16717127 The origin and maintenance of mammalian peroxisomes involves...	ACCEPT	Summary: Kim et al. (2006) showed by fluorescence microscopy and cell fractionation that PEX16-GFP localizes to ER membranes in addition to peroxisomes. In cells lacking peroxisomes (PBD399-T1 or PBD400), PEX16-GFP was exclusively in the ER. In vitro assays confirmed cotranslational insertion into ER microsomes. FLIP experiments showed PEX16-GFP diffuses freely throughout the ER. Reason: ER membrane is a bona fide localization of PEX16, representing the site of its cotranslational insertion and a transit point during trafficking to peroxisomes. Strong experimental evidence from imaging, fractionation, and in vitro insertion assays. Supporting Evidence: PMID:16717127 The distribution of PEX16-GFP in these cells included the ER as well as peroxisomes PMID:16717127 a significant proportion of PEX16-glyc molecules underwent glycosylation during cotranslational targeting, whereas none did so during posttranslational targeting. The data thus confirmed that PEX16 undergoes cotranslational insertion into the ER
GO:0005778 peroxisomal membrane	IDA PMID:12223482 The membrane biogenesis peroxin Pex16p. Topogenesis and func...	ACCEPT	Summary: Honsho et al. (2002) determined the membrane topology of PEX16 by differential permeabilization, showing it is an integral peroxisomal membrane protein with both N- and C-terminal domains exposed to the cytosol. They identified the topogenic sequence (residues 66-81 and the first transmembrane segment) essential for membrane integration. Reason: Direct experimental evidence for peroxisomal membrane localization and topology determination. This is a primary characterization study. Supporting Evidence: PMID:12223482 we have determined the membrane topology of Pex16p by differential permeabilization method: both N- and C-terminal parts are exposed to the cytosol
GO:0016557 peroxisome membrane biogenesis	IMP PMID:12223482 The membrane biogenesis peroxin Pex16p. Topogenesis and func...	ACCEPT	Summary: Honsho et al. (2002) showed that overexpression of dysfunctional PEX16 variants interfered with peroxisome membrane assembly. The C-terminal cytoplasmic part of PEX16 abrogated peroxisome restoration in pex3 mutants, implying PEX16 functions upstream of PEX3 in peroxisome membrane assembly. Reason: Functional evidence that PEX16 is required for peroxisome membrane biogenesis, acting upstream of PEX3 in the pathway. Supporting Evidence: PMID:12223482 Pex16p C-terminal cytoplasmic part severely abrogated peroxisome restoration in pex mutants such as matrix protein import-defective pex12 and membrane assembly impaired pex3 by respective PEX12 and PEX3 expression
GO:0045046 protein import into peroxisome membrane	IMP PMID:12223482 The membrane biogenesis peroxin Pex16p. Topogenesis and func...	ACCEPT	Summary: Honsho et al. (2002) showed that dysfunctional PEX16 variants interfered with localization of PMPs (Pex14p, Pex13p, PMP70) to peroxisomes, demonstrating that PEX16 is required for PMP import into the peroxisome membrane. Reason: Direct evidence that PEX16 function is required for import of PMPs (Pex14p, Pex13p, PMP70) into the peroxisome membrane. This is a core function annotation. Supporting Evidence: PMID:12223482 Localization to peroxisomes of membrane proteins such as Pex14p, Pex13p, and PMP70 was interfered with in CHO-K1 cells by a higher level expression of the pex16 patient-derived dysfunctional but topogenically active Pex16pR176ter
GO:0005777 peroxisome	IDA PMID:15813749 Requirement for microtubules and dynein motors in the earlie...	ACCEPT	Summary: Brocard et al. (2005) used PEX16-mutant cells for microinjection complementation studies examining microtubule requirements for peroxisome biogenesis. PEX16 was expressed and localized to newly formed peroxisomes in complemented cells. Reason: Peroxisome localization of PEX16 confirmed in the context of complementation experiments. Supporting Evidence: PMID:15813749 nuclear microinjection of plasmids expressing EGFP-SKL and Pex16p in PEX16-mutant cells resulted in the accumulation of EGFP-SKL into newly formed peroxisomes
GO:0007031 peroxisome organization	IMP PMID:15813749 Requirement for microtubules and dynein motors in the earlie...	ACCEPT	Summary: Brocard et al. (2005) showed that PEX16 complementation in PEX16-mutant cells restores peroxisome formation, and that this process requires microtubules and dynein motors. This demonstrates PEX16's role in peroxisome organization. Reason: Complementation of PEX16-mutant cells demonstrates PEX16 is required for peroxisome organization. The paper adds mechanistic context (microtubule dependence). Supporting Evidence: PMID:15813749 pretreatment of the cells with nocodazol, prior to microinjection, resulted in the inhibition of complementation of the PEX16 mutant
GO:0005778 peroxisomal membrane	IMP PMID:9922452 Peroxisome synthesis in the absence of preexisting peroxisom...	ACCEPT	Summary: South and Gould (1999) showed that PBD061 cells (PEX16-deficient) lack detectable peroxisome membranes and cannot import PMPs. Expression of PEX16 restores peroxisome membranes. This demonstrates PEX16 is required for peroxisomal membrane formation. However, the evidence type IMP with CC term is unusual -- this represents the mutant phenotype showing PEX16 is required for peroxisomal membrane existence. Reason: Mutant phenotype demonstrates PEX16 is essential for peroxisomal membrane formation. PEX16-deficient cells completely lack peroxisomal membranes. Supporting Evidence: PMID:9922452 we report here a Zellweger syndrome patient (PBD061) with an unusual cellular phenotype, an inability to import peroxisomal membrane proteins PMID:9922452 expression of PEX16 restores the formation of new peroxisomes in PBD061 cells
GO:0016558 protein import into peroxisome matrix	IMP PMID:9922452 Peroxisome synthesis in the absence of preexisting peroxisom...	MARK AS OVER ANNOTATED	Summary: South and Gould (1999) showed that PBD061 (PEX16-deficient) cells are unable to import peroxisomal matrix proteins because they lack peroxisomes entirely. After PEX16 complementation, matrix protein import was restored following membrane assembly. However, PEX16 is not directly involved in matrix protein import -- it is required for membrane biogenesis, which is prerequisite for matrix import. This annotation conflates an indirect downstream effect with a direct function. Reason: PEX16 is not directly involved in peroxisome matrix protein import. Its role is in membrane biogenesis. The inability to import matrix proteins in PEX16-deficient cells is an indirect consequence of having no peroxisomal membranes. The direct function is peroxisome membrane biogenesis (GO:0016557), which is already annotated. South and Gould (1999) themselves noted: "Peroxisome synthesis and peroxisomal membrane protein import could be detected within 2-3 h of PEX16 injection and was followed by matrix protein import" -- showing matrix import is a downstream consequence, not a direct PEX16 function. Supporting Evidence: PMID:9922452 Peroxisome synthesis and peroxisomal membrane protein import could be detected within 2-3 h of PEX16 injection and was followed by matrix protein import
GO:0060090 molecular adaptor activity	IDA PMID:19114594 The peroxisomal membrane protein import receptor Pex3p is di...	NEW	Summary: PEX16 functions as a molecular adaptor/receptor at the peroxisomal membrane, bringing together PEX3 and PEX19 in a trimeric complex to enable PMP delivery. Matsuzaki and Fujiki (2008) demonstrated that PEX16 is the membrane receptor for PEX3-PEX19 complexes using semi-intact cell import assays. Lee et al. (2024) confirmed a specific PEX3-PEX16 interface (PEX16 loop residues 132-214) with PEX19 binding PEX3 on the opposite face, supporting a trimeric adaptor model. This MF term is not currently annotated in GOA but accurately describes PEX16's core molecular function of bridging PEX3 and PEX19 at the membrane. Reason: PEX16 acts as a molecular adaptor by bringing together PEX3 (via direct binding through its cytosolic loop) and PEX19 (indirectly, through the PEX3-PEX19 interaction) at the peroxisomal membrane. This adaptor/scaffold function is the core molecular activity of PEX16. The existing 'protein binding' annotations are uninformative, and 'protein to membrane docking' (GO:0022615) is a BP term. GO:0060090 (molecular adaptor activity) best captures PEX16's role as a membrane-anchored receptor that coordinates the PEX3-PEX16-PEX19 assembly for PMP delivery. Supporting Evidence: PMID:19114594 we demonstrate that Pex16p functions as the Pex3p-docking site and serves as the peroxisomal membrane receptor that is specific to the Pex3p-Pex19p complexes PMID:19114594 Pex16p was a prerequisite for peroxisomal targeting of newly synthesized Pex3p in vivo, functioning as the Pex3p membrane receptor

Core Functions

PEX16 is an integral peroxisomal membrane peroxin that functions as the membrane receptor/docking site for PEX3-PEX19 complexes. PEX16 binds PEX3 directly via a cytosolic loop (residues 132-214) and enables PMP delivery to the peroxisomal membrane. PEX16 is essential for peroxisome membrane biogenesis; loss of PEX16 leads to complete absence of peroxisomal membranes and causes Zellweger spectrum disorders (complementation group 9). PEX16 also mediates ER-dependent de novo peroxisome formation by being cotranslationally inserted into the ER and recruiting other PMPs (PEX3, PMP34) to ER membranes for subsequent transport to peroxisomes.

Molecular Function:

molecular adaptor activity

Directly Involved In:

peroxisome membrane biogenesis ER-dependent peroxisome organization protein import into peroxisome membrane peroxisome organization

Cellular Locations:

peroxisomal membrane endoplasmic reticulum membrane

Supporting Evidence:

PMID:19114594
we demonstrate that Pex16p functions as the Pex3p-docking site and serves as the peroxisomal membrane receptor that is specific to the Pex3p-Pex19p complexes
PMID:16717127
We provide direct evidence that peroxisomes can arise de novo from the ER in both normal and peroxisome-less mutant cells. We further show that PEX16 regulates this process by being cotranslationally inserted into the ER and serving to recruit other peroxisomal membrane proteins to membranes.
PMID:9837814
HsPEX16 expression morphologically and biochemically restored peroxisome biogenesis only in fibroblasts from a CG-D patient with ZS

References

GO_REF:0000033

Annotation inferences using phylogenetic trees

GO_REF:0000043

Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:12223482

The membrane biogenesis peroxin Pex16p. Topogenesis and functional roles in peroxisomal membrane assembly.

PEX16 membrane topology determined -- both N and C termini cytosolic, two transmembrane segments
Residues 66-81 and first TM segment required for peroxisomal membrane integration
Dysfunctional PEX16 variants interfere with PMP localization (Pex14p, Pex13p, PMP70)
PEX16 C-terminal domain abrogates peroxisome restoration in pex3 and pex12 mutants

PMID:14709540

PEX19 is a predominantly cytosolic chaperone and import receptor for class 1 peroxisomal membrane proteins.

PEX19 binds and stabilizes newly synthesized PMPs including PEX16 in the cytosol
PEX16 contains two mPTS regions bound by PEX19 (aa 59-219 and aa 221-336)
PEX19 functions as both chaperone and import receptor for class 1 PMPs
Inhibition of PEX19 causes specific PMP import defect

PMID:15713480

Analysis of human Pex19p's domain structure by pentapeptide scanning mutagenesis.

PEX19 carboxy-terminal domain interacts with PEX16 among other PMPs
PEX19 has tripartite domain structure with PEX3-binding, PEX14-binding, and PMP-binding domains

PMID:15813749

Requirement for microtubules and dynein motors in the earliest stages of peroxisome biogenesis.

PEX16 complementation of mutant cells requires microtubules and dynein motors
Nocodazol and dominant-negative dynactin prevent PEX16-mediated peroxisome restoration

PMID:16717127

The origin and maintenance of mammalian peroxisomes involves a de novo PEX16-dependent pathway from the ER.

PEX16 is cotranslationally inserted into the ER
PEX16 traffics from ER to peroxisomes (photoactivation pulse-chase)
PEX16 recruits PEX3 and PMP34 to ER membranes
PEX16 with signal anchor sequence complements PEX16-deficient cells from ER
New peroxisomes derive primarily from ER in growing cells

PMID:19114594

The peroxisomal membrane protein import receptor Pex3p is directly transported to peroxisomes by a novel Pex19p- and Pex16p-dependent pathway.

PEX16 functions as the membrane receptor for PEX3-PEX19 complexes
Ectopic PEX16 expression enhances PEX3 targeting 5-6 fold
PEX16 knockdown abrogates PEX3 peroxisomal targeting
PEX3 mPTS directly binds PEX16 (co-IP of cell-free synthesized proteins)
Both N- and C-terminal regions of PEX16 indispensable for recruiting PEX3-PEX19 complexes

PMID:19479899

Pex3p-dependent peroxisomal biogenesis initiates in the endoplasmic reticulum of human fibroblasts.

Pex3p requires Pex16p for ER location but not vice versa
Pex3p follows ER-to-peroxisome route in mammalian cells
De novo peroxisome biogenesis involves ER intermediate

PMID:19946888

Defining the membrane proteome of NK cells.

Large-scale proteomics study identifying PEX16 in membrane fraction of NK cells

PMID:21525035

PEX14 is required for microtubule-based peroxisome motility in human cells.

PEX16 identified as peroxisomal membrane protein by mass spectrometry in PEX14 complex isolation

PMID:21768384

Sec16B is involved in the endoplasmic reticulum export of the peroxisomal membrane biogenesis factor peroxin 16 (Pex16) in mammalian cells.

Sec16B required for ER-to-peroxisome transport of PEX16
Sec16B knockdown causes PEX16 redistribution to ER and peroxisome elongation
PEX16 Sec16B-dependent trafficking links ER exit site machinery to peroxisome biogenesis

PMID:9837814

Mutation in PEX16 is causal in the peroxisome-deficient Zellweger syndrome of complementation group D.

PEX16 identified as causative gene for CG-D (CG-IX) Zellweger syndrome
PEX16 encodes 336 amino acid peroxisomal protein
R176ter nonsense mutation found in patient
PEX16 expression restores peroxisome biogenesis in CG-D patient fibroblasts

PMID:9922452

Peroxisome synthesis in the absence of preexisting peroxisomes.

PBD061 cells (PEX16-deficient) lack peroxisomal membranes and cannot import PMPs
PEX16 expression restores peroxisome formation de novo
PMP import precedes matrix protein import after PEX16 complementation
Peroxisomes can form without preexisting peroxisomes

Reactome:R-HSA-9603775

PEX3:PEX19:class I PMP dissociates

Reactome:R-HSA-9603784

PEX19:class I PMP binds PEX3

Reactome:R-HSA-9603804

PEX19 binds class I peroxisomal membrane proteins

Reactome:R-NUL-9604086

PEX19:Pex3 binds PEX16

Reactome:R-NUL-9604116

PEX16:PEX19:Pex3 dissociates

Deep Research

Falcon

(PEX16-deep-research-falcon.md)

Research Report: Human **PEX16** (UniProt **Q9Y5Y5**) — Functional Annotation, Mechanism, and Disease Relevance Falcon Edison Scientific Literature 37 citations 2026-03-05T04:21:59.160383

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research Report: Human PEX16 (UniProt Q9Y5Y5) — Functional Annotation, Mechanism, and Disease Relevance

0) Target verification (critical identity check)

The gene/protein discussed here is human PEX16 (UniProt Q9Y5Y5), annotated as Peroxisomal membrane protein PEX16 / Peroxin-16 / Peroxisomal biogenesis factor 16. The literature synthesized below consistently treats PEX16 as an integral peroxisomal membrane peroxin acting in peroxisome membrane biogenesis, aligning with the UniProt-provided description and peroxin-16 family assignment (Kim et al., 2006; Fujiki et al., 2014; Okumoto et al., 2021; Lee et al., 2024) (kim2006theoriginand pages 1-2, fujiki2014peroxisomebiogenesisin pages 2-4, okumoto2021peroxisomemetabolicfunctions pages 52-54, lee2024systematicdiscoveryof pages 11-12).

1) Key concepts and definitions (current understanding)

1.1 Peroxisome biogenesis and “early peroxins”

Peroxisomes are single-membrane organelles; their biogenesis requires a conserved set of PEX genes encoding “peroxins.” In classic mammalian frameworks, PEX3, PEX16, and PEX19 are grouped as “early” peroxins central to peroxisomal membrane protein (PMP) biogenesis and membrane assembly (fujiki2014peroxisomebiogenesisin pages 2-4, kim2013pex16amultifaceted pages 1-2, okumoto2021peroxisomemetabolicfunctions pages 52-54).

Authoritative reviews describe two mechanistic classes/pathways for membrane assembly in mammals, in which PEX16 is positioned with PEX3 and PEX19 as membrane biogenesis factors (fujiki2014peroxisomebiogenesisin pages 2-4, okumoto2021peroxisomemetabolicfunctions pages 52-54).

1.2 Molecular function of PEX16 (functional definition)

PEX16 is best understood as a membrane biogenesis factor/adaptor/receptor that enables the establishment and maintenance of peroxisomal membranes by coordinating trafficking and/or docking of PMPs—particularly via functional coupling with PEX3 and PEX19 (kim2006theoriginand pages 1-2, aranovich2014pex16contributesto pages 1-2, farre2017anewyeast pages 6-11).

A concise functional definition supported by mechanistic evidence is:
- PEX16 is an integral membrane peroxin that participates in ER-linked de novo peroxisome formation and ongoing PMP trafficking/maintenance, acting in concert with PEX3 and the cytosolic PMP chaperone/receptor PEX19 (kim2006theoriginand pages 1-2, aranovich2014pex16contributesto pages 1-2, yonekawa2011sec16bisinvolved pages 1-2).

2) Subcellular localization and trafficking routes

2.1 ER-to-peroxisome route for PEX16 and PMP delivery

A landmark live-cell study provided direct evidence that mammalian peroxisomes can form de novo from the ER, and that PEX16 regulates this process. Key observations included:
- PEX16 is cotranslationally inserted into the ER and helps recruit other PMPs to membranes during peroxisome formation (kim2006theoriginand pages 1-2).
- In peroxisome-deficient contexts (including PEX16 mutant cells and other PBD lines lacking PEX3 or PEX19), fluorescently tagged PEX16 localized to the ER, supporting ER residence as an intermediate when peroxisomes are absent (kim2006theoriginand pages 2-3).
- Biochemical fractionation supported that PEX16 fusion proteins were membrane-associated (nonsoluble fraction), and not cytosolic (kim2006theoriginand pages 2-3).

2.2 PEX16 in peroxisome maintenance via ER trafficking

Beyond de novo formation, quantitative live-cell microscopy showed that the ER can constitutively supply membrane components to existing peroxisomes and that PEX16 mediates ER-dependent trafficking of other PMPs. Specifically, PEX16 was reported to mediate ER-associated trafficking of PEX3 and PMP34 to peroxisomes (aranovich2014pex16contributesto pages 1-2).

2.3 ER export machinery involvement (Sec16B)

Mechanistic work in mammalian cells identified Sec16B as an ER-associated factor required for export of PEX16 from the ER to peroxisomes. Perturbing Sec16B affected PEX16 transport and peroxisome morphology, implicating ER exit site machinery in PEX16 trafficking and peroxisome membrane biogenesis (yonekawa2011sec16bisinvolved pages 1-2).

3) Interaction partners and molecular assembly (PEX3–PEX19–PEX16)

3.1 Canonical module: PEX19 (cytosolic carrier) → PEX3/PEX16 (membrane receptors)

Reviews and mechanistic models place PEX16 in the PMP targeting pathway alongside:
- PEX19, a cytosolic receptor/chaperone for newly synthesized PMPs
- PEX3, a membrane docking receptor for PEX19–PMP complexes
- PEX16, proposed to act as a receptor for PEX3 and/or facilitate PMP recruitment at the ER/peroxisome membranes
(kim2006theoriginand pages 1-2, fujiki2014peroxisomebiogenesisin pages 2-4, kim2013pex16amultifaceted pages 1-2, okumoto2021peroxisomemetabolicfunctions pages 52-54).

3.2 2024 structural/interface advance: validated PEX3–PEX16 interface and trimer model

A 2024 Molecular Systems Biology study used AlphaFold-based interface prediction and experimental validation (BRET) to refine how this module assembles:
- PEX16 contains a large loop (residues ~132–214) predicted with high confidence to bind a pocket on PEX3; multiple fragments and full-length PEX16 were repeatedly predicted to bind similarly, increasing confidence (lee2024systematicdiscoveryof pages 11-12).
- Experimental perturbations (PEX16 loop deletions such as del162–192 and point mutants) and PEX3 mutations (R54S, E272R) reduced PEX3–PEX16 binding signals, while those PEX3 mutants did not disrupt PEX3–PEX19 binding—supporting a specific interface rather than global misfolding (lee2024systematicdiscoveryof pages 11-12).
- The authors propose a trimeric complex in which PEX16 anchors PEX3 at the peroxisomal membrane, while PEX19 binds PEX3 on the opposite face and can deliver PMPs (lee2024systematicdiscoveryof pages 11-12, lee2024systematicdiscoveryof media 501987af).

This study explicitly argues that such structural models can help interpret many currently uncharacterized variants in PEX genes (lee2024systematicdiscoveryof pages 11-12).

4) Recent developments and latest research (prioritizing 2023–2024)

4.1 Variant interpretation and mechanistic clarity via interface mapping (2024)

The 2024 PEX3–PEX16/PEX3–PEX19 interface work is a key recent development because it:
- provides an experimentally supported physical model for how PEX16 participates in anchoring PEX3 and enabling PMP delivery,
- identifies concrete interface regions (loop and pockets) that are plausible hotspots for pathogenic missense variants, and
- connects structure to disease variant interpretation frameworks (lee2024systematicdiscoveryof pages 11-12, lee2024systematicdiscoveryof media 501987af).

4.2 2024 review context: peroxisome biology as an active frontier

A 2024 comprehensive review (“mysteries 3.0”) emphasizes continued advances in peroxisome biology, including protein import and regulation, underscoring that peroxisome biogenesis and trafficking remain areas with open mechanistic questions (kumar2024theperoxisomean pages 10-11). While this portion of the review text captured here focuses on matrix import (PEX5/PEX13/PEX14), it provides the up-to-date framing that peroxisome assembly mechanisms remain actively refined.

5) Disease relevance: Zellweger spectrum / peroxisome biogenesis disorders (PBDs)

5.1 PEX16 is a PBD gene (Complementation Group 9)

Classic human genetics literature assigns PEX16 as the causative gene for Complementation Group 9 (CG9) within the Zellweger spectrum disorders (ZSD), with PEX16 described as a ~39 kDa peroxisomal membrane protein required for PMP import (gould2000peroxisomebiogenesisdisorders pages 1-2).

Later mammalian-focused reviews retain this mapping: PEX16 is listed as CG9 (Japan designation D) associated with Zellweger syndrome (ZS) (fujiki2014peroxisomebiogenesisin pages 2-4, okumoto2021peroxisomemetabolicfunctions pages 52-54).

5.2 Cellular phenotypes in PEX16-deficient patient cells and rescue

Patient-derived fibroblasts defective in PEX16 can show absence of detectable peroxisomes, and introduction of PEX16 fusion constructs can restore the appearance of new peroxisomes, providing a direct functional complementation phenotype (kim2006theoriginand pages 2-3, kim2006theoriginand pages 1-2).

A mammalian review table also indicates “peroxisome ghosts” are absent (ghost “−”) in the PEX16 CG9 context, consistent with loss of peroxisomal membrane structures when PEX16 function is disrupted (fujiki2014peroxisomebiogenesisin pages 2-4).

6) Current applications and real-world implementations

6.1 Clinical genetics: diagnosis and classification

PEX16 is used in the diagnostic and classification ecosystem for ZSD/PBDs through the established connection to CG9 and Zellweger syndrome terminology (gould2000peroxisomebiogenesisdisorders pages 1-2, fujiki2014peroxisomebiogenesisin pages 2-4, okumoto2021peroxisomemetabolicfunctions pages 52-54).

6.2 Variant interpretation and mechanistic annotation

A practical, emerging application (explicitly stated in 2024 work) is the use of structure-informed interaction interfaces (PEX3–PEX16; trimer model) to interpret disease variants and guide follow-up functional assays, because many annotated variants across PEX genes remain uncharacterized (lee2024systematicdiscoveryof pages 11-12).

6.3 Cell biology toolkits and model systems

PEX16-dependent phenotypes are used as experimental readouts in:
- live-cell imaging of ER-to-peroxisome trafficking and peroxisome regeneration (kim2006theoriginand pages 2-3),
- perturbation of ER export machinery (Sec16B) to modulate peroxisome membrane biogenesis (yonekawa2011sec16bisinvolved pages 1-2),
- assays quantifying PMP trafficking via ER (PEX3, PMP34) to understand peroxisome maintenance (aranovich2014pex16contributesto pages 1-2).

7) Expert synthesis and analysis (authoritative perspectives)

7.1 Consensus vs evolving points

Across primary studies and reviews, a stable consensus is that PEX16 participates in peroxisomal membrane assembly/biogenesis with PEX3 and PEX19 (fujiki2014peroxisomebiogenesisin pages 2-4, okumoto2021peroxisomemetabolicfunctions pages 52-54, kim2006theoriginand pages 1-2). The route and relative importance of ER involvement has evolved: strong evidence supports ER participation in de novo formation and in at least some ongoing trafficking/maintenance, with PEX16 a central mediator (kim2006theoriginand pages 1-2, aranovich2014pex16contributesto pages 1-2, yonekawa2011sec16bisinvolved pages 1-2).

The 2024 interface study adds an expert-level refinement: PEX16 is not merely “involved,” but can be modeled as an anchoring receptor for PEX3, using a defined cytosolic loop that binds PEX3 and allows PEX3 to simultaneously bind PEX19, yielding a coherent assembly model for PMP delivery at the peroxisomal membrane (lee2024systematicdiscoveryof pages 11-12, lee2024systematicdiscoveryof media 501987af).

8) Key statistics and quantitative data points (from available sources)

PEX16 protein size: ~39 kDa in CG tables/reviews (gould2000peroxisomebiogenesisdisorders pages 1-2, fujiki2014peroxisomebiogenesisin pages 2-4).
Complementation group: CG9 (Zellweger syndrome association) (gould2000peroxisomebiogenesisdisorders pages 1-2, fujiki2014peroxisomebiogenesisin pages 2-4, okumoto2021peroxisomemetabolicfunctions pages 52-54).
Historical patient count in one classic review cohort: CG9 shows 1 Zellweger syndrome patient attributed to PEX16 in that table (gould2000peroxisomebiogenesisdisorders pages 1-2).
Imaging/biochemical timepoints used in mechanistic study: analyses including fractionation at 24 h post-transfection (with expression also discussed as 15–24 h) (kim2006theoriginand pages 2-3).
2024 interface mapping residue ranges: PEX16 loop ~132–214 implicated; deletion del162–192 tested; PEX16 fold described across residues 19–286 (lee2024systematicdiscoveryof pages 11-12).

9) Evidence figure

A key visual support for the 2024 mechanistic advance is the extracted figure region showing the predicted interfaces, BRET binding perturbations, and proposed trimer assembly model (lee2024systematicdiscoveryof media 501987af).

Embedded evidence table (key papers, dates, URLs)

Reference & Year	System / Method	Key Findings / Mechanism	Disease / Clinical Link	DOI / Link
Lee et al. (2024)	AlphaFold, BRET, Human Cells	Predicted and validated a trimeric complex where PEX16 anchors PEX3 to the peroxisome membrane via a specific loop (residues 132–214). PEX19 binds PEX3 opposite to PEX16.	Notes that mutations in PEX proteins (PEX3/16/19) cause PBDs and structural data helps map these variants.	10.1038/s44320-023-00005-6 (lee2024systematicdiscoveryof pages 11-12)
Fatima et al. (2024)	Human Cells (Screen)	Identifies PEX16 assembly at the ER as an early step in de novo biogenesis, facilitated by the ER protein RRBP1.	N/A	10.1242/jcs.264075 (fatima2024ribosomebindingprotein1 pages 1-2)
Okumoto et al. (2021)	Review (Mammalian)	Summarizes PEX16's role in the Class I pathway: Pex19p transports PMPs to Pex3p, forming the membrane. Lists PEX16 as Complementation Group 9 (CG9).	Assigns PEX16 to CG9 (Group D), associated with Zellweger Syndrome.	10.1007/978-3-030-60204-8_1 (okumoto2021peroxisomemetabolicfunctions pages 52-54)
Fujiki et al. (2014)	Review (Mammalian)	Describes PEX16 as one of three "early peroxins" (with PEX3, PEX19) exclusively required for membrane assembly.	Confirms PEX16 defects lead to absence of peroxisome ghosts (Ghost (-) phenotype) in CG9.	10.3389/fphys.2014.00307 (fujiki2014peroxisomebiogenesisin pages 2-4)
Aranovich et al. (2014)	Human Cells	Demonstrated that PEX16 mediates ER-to-peroxisome trafficking of PEX3 and PMP34, supporting a role in peroxisome maintenance via the ER.	Discusses implications for Peroxisome Biogenesis Disorders where membrane assembly fails.	10.1242/jcs.146282 (aranovich2014pex16contributesto pages 1-2)
Yonekawa et al. (2011)	Mammalian Cells	Found that Sec16B is required for the export of PEX16 from the ER to peroxisomes, linking ERES machinery to peroxisome biogenesis.	N/A	10.1073/pnas.1103283108 (yonekawa2011sec16bisinvolved pages 1-2)
Kim et al. (2006)	Human Fibroblasts	Provided direct evidence that PEX16 travels from the ER to peroxisomes and is essential for de novo formation. Reintroduction restores peroxisomes in PEX16-deficient cells.	Used PBD patient cells (GM06231) to demonstrate phenotype of absent peroxisomes and rescue by PEX16-GFP.	10.1083/jcb.200601036 (kim2006theoriginand pages 1-2)
Gould & Valle (2000)	Review (Human)	Established PEX16 as the causative gene for Complementation Group 9 (CG9) in the Zellweger spectrum.	Identified PEX16 mutation in a Zellweger syndrome patient (CG9).	10.1016/s0168-9525(00)02056-4 (gould2000peroxisomebiogenesisdisorders pages 1-2)

Table: A summary of key literature establishing PEX16 as an essential ER-associated peroxin involved in membrane biogenesis, its structural interactions with PEX3/PEX19, and its role in Zellweger spectrum disorders (Complementation Group 9).

References (URLs and publication dates)

The report cites the following key sources (see artifact table for DOIs/URLs):
- Gould & Valle. Trends in Genetics. Aug 2000. https://doi.org/10.1016/S0168-9525(00)02056-4 (gould2000peroxisomebiogenesisdisorders pages 1-2)
- Kim et al. J Cell Biol. May 2006. https://doi.org/10.1083/jcb.200601036 (kim2006theoriginand pages 1-2, kim2006theoriginand pages 2-3)
- Yonekawa et al. PNAS. Jul 2011. https://doi.org/10.1073/pnas.1103283108 (yonekawa2011sec16bisinvolved pages 1-2)
- Aranovich et al. J Cell Sci. Sep 2014. https://doi.org/10.1242/jcs.146282 (aranovich2014pex16contributesto pages 1-2)
- Fujiki et al. Front Physiol. Aug 2014. https://doi.org/10.3389/fphys.2014.00307 (fujiki2014peroxisomebiogenesisin pages 2-4)
- Okumoto et al. Adv Exp Med Biol. Jan 2021. https://doi.org/10.1007/978-3-030-60204-8_1 (okumoto2021peroxisomemetabolicfunctions pages 52-54)
- Kumar et al. Histochem Cell Biol. Jan 2024. https://doi.org/10.1007/s00418-023-02259-5 (kumar2024theperoxisomean pages 10-11)
- Lee et al. Molecular Systems Biology. Jan 2024. https://doi.org/10.1038/s44320-023-00005-6 (lee2024systematicdiscoveryof pages 11-12, lee2024systematicdiscoveryof pages 12-13, lee2024systematicdiscoveryof media 501987af)

References

(kim2006theoriginand pages 1-2): Peter K. Kim, Robert T. Mullen, Uwe Schumann, and Jennifer Lippincott-Schwartz. The origin and maintenance of mammalian peroxisomes involves a de novo pex16-dependent pathway from the er. The Journal of Cell Biology, 173:521-532, May 2006. URL: https://doi.org/10.1083/jcb.200601036, doi:10.1083/jcb.200601036. This article has 463 citations.
(fujiki2014peroxisomebiogenesisin pages 2-4): Yukio Fujiki, Kanji Okumoto, Satoru Mukai, Masanori Honsho, and Shigehiko Tamura. Peroxisome biogenesis in mammalian cells. Frontiers in Physiology, Aug 2014. URL: https://doi.org/10.3389/fphys.2014.00307, doi:10.3389/fphys.2014.00307. This article has 168 citations.
(okumoto2021peroxisomemetabolicfunctions pages 52-54): Kanji Okumoto, Shigehiko Tamura, Masanori Honsho, and Yukio Fujiki. Peroxisome: metabolic functions and biogenesis. Advances in experimental medicine and biology, 1299:3-17, Jan 2021. URL: https://doi.org/10.1007/978-3-030-60204-8_1, doi:10.1007/978-3-030-60204-8_1. This article has 100 citations and is from a peer-reviewed journal.
(lee2024systematicdiscoveryof pages 11-12): Chop Yan Lee, Dalmira Hubrich, Julia K Varga, Christian Schäfer, Mareen Welzel, Eric Schumbera, Milena Djokic, Joelle M Strom, Jonas Schönfeld, Johanna L Geist, Feyza Polat, Toby J Gibson, Claudia Isabelle Keller Valsecchi, Manjeet Kumar, Ora Schueler-Furman, and Katja Luck. Systematic discovery of protein interaction interfaces using alphafold and experimental validation. Jan 2024. URL: https://doi.org/10.1038/s44320-023-00005-6, doi:10.1038/s44320-023-00005-6. This article has 95 citations and is from a highest quality peer-reviewed journal.
(kim2013pex16amultifaceted pages 1-2): Peter K. Kim and Robert T. Mullen. Pex16: a multifaceted regulator of peroxisome biogenesis. Frontiers in Physiology, Aug 2013. URL: https://doi.org/10.3389/fphys.2013.00241, doi:10.3389/fphys.2013.00241. This article has 52 citations.
(aranovich2014pex16contributesto pages 1-2): Alexander Aranovich, Rong Hua, Andrew D. Rutenberg, and Peter K. Kim. Pex16 contributes to peroxisome maintenance by constantly trafficking pex3 via the er. Journal of Cell Science, 127:3675-3686, Sep 2014. URL: https://doi.org/10.1242/jcs.146282, doi:10.1242/jcs.146282. This article has 103 citations and is from a domain leading peer-reviewed journal.
(farre2017anewyeast pages 6-11): Jean-Claude Farré, Krypton Carolino, Oleh V. Stasyk, Olena G. Stasyk, Zlatan Hodzic, Gaurav Agrawal, Andreas Till, Marco Proietto, James Cregg, Andriy A. Sibirny, and Suresh Subramani. A new yeast peroxin, pex36, a functional homolog of mammalian pex16, functions in the er-to-peroxisome traffic of peroxisomal membrane proteins. Journal of molecular biology, 429 23:3743-3762, Nov 2017. URL: https://doi.org/10.1016/j.jmb.2017.10.009, doi:10.1016/j.jmb.2017.10.009. This article has 43 citations and is from a domain leading peer-reviewed journal.
(yonekawa2011sec16bisinvolved pages 1-2): Shusuke Yonekawa, Akiko Furuno, Takashi Baba, Yukio Fujiki, Yuta Ogasawara, Akitsugu Yamamoto, Mitsuo Tagaya, and Katsuko Tani. Sec16b is involved in the endoplasmic reticulum export of the peroxisomal membrane biogenesis factor peroxin 16 (pex16) in mammalian cells. Proceedings of the National Academy of Sciences, 108:12746-12751, Jul 2011. URL: https://doi.org/10.1073/pnas.1103283108, doi:10.1073/pnas.1103283108. This article has 107 citations and is from a highest quality peer-reviewed journal.
(kim2006theoriginand pages 2-3): Peter K. Kim, Robert T. Mullen, Uwe Schumann, and Jennifer Lippincott-Schwartz. The origin and maintenance of mammalian peroxisomes involves a de novo pex16-dependent pathway from the er. The Journal of Cell Biology, 173:521-532, May 2006. URL: https://doi.org/10.1083/jcb.200601036, doi:10.1083/jcb.200601036. This article has 463 citations.
(lee2024systematicdiscoveryof media 501987af): Chop Yan Lee, Dalmira Hubrich, Julia K Varga, Christian Schäfer, Mareen Welzel, Eric Schumbera, Milena Djokic, Joelle M Strom, Jonas Schönfeld, Johanna L Geist, Feyza Polat, Toby J Gibson, Claudia Isabelle Keller Valsecchi, Manjeet Kumar, Ora Schueler-Furman, and Katja Luck. Systematic discovery of protein interaction interfaces using alphafold and experimental validation. Jan 2024. URL: https://doi.org/10.1038/s44320-023-00005-6, doi:10.1038/s44320-023-00005-6. This article has 95 citations and is from a highest quality peer-reviewed journal.
(kumar2024theperoxisomean pages 10-11): Rechal Kumar, Markus Islinger, Harley Worthy, Ruth Carmichael, and Michael Schrader. The peroxisome: an update on mysteries 3.0. Histochemistry and Cell Biology, 161:99-132, Jan 2024. URL: https://doi.org/10.1007/s00418-023-02259-5, doi:10.1007/s00418-023-02259-5. This article has 73 citations and is from a peer-reviewed journal.
(gould2000peroxisomebiogenesisdisorders pages 1-2): Stephen J Gould and David Valle. Peroxisome biogenesis disorders: genetics and cell biology. Trends in genetics : TIG, 16 8:340-5, Aug 2000. URL: https://doi.org/10.1016/s0168-9525(00)02056-4, doi:10.1016/s0168-9525(00)02056-4. This article has 560 citations.
(fatima2024ribosomebindingprotein1 pages 1-2): Kaneez Fatima, Helena Vihinen, Ani Akpinar, Tamara Somborac, Anja Paatero, Eija Jokitalo, Ville Paavilainen, Pekka Katajisto, and Svetlana Konovalova. Ribosome-binding protein 1 maintains peroxisome biogenesis. Journal of Cell Science, Dec 2024. URL: https://doi.org/10.1242/jcs.264075, doi:10.1242/jcs.264075. This article has 1 citations and is from a domain leading peer-reviewed journal.
(lee2024systematicdiscoveryof pages 12-13): Chop Yan Lee, Dalmira Hubrich, Julia K Varga, Christian Schäfer, Mareen Welzel, Eric Schumbera, Milena Djokic, Joelle M Strom, Jonas Schönfeld, Johanna L Geist, Feyza Polat, Toby J Gibson, Claudia Isabelle Keller Valsecchi, Manjeet Kumar, Ora Schueler-Furman, and Katja Luck. Systematic discovery of protein interaction interfaces using alphafold and experimental validation. Jan 2024. URL: https://doi.org/10.1038/s44320-023-00005-6, doi:10.1038/s44320-023-00005-6. This article has 95 citations and is from a highest quality peer-reviewed journal.

Citations

kim2006theoriginand pages 1-2
kim2006theoriginand pages 2-3
lee2024systematicdiscoveryof pages 11-12
kumar2024theperoxisomean pages 10-11
gould2000peroxisomebiogenesisdisorders pages 1-2
fujiki2014peroxisomebiogenesisin pages 2-4
okumoto2021peroxisomemetabolicfunctions pages 52-54
farre2017anewyeast pages 6-11
lee2024systematicdiscoveryof pages 12-13
10.1038/s44320-023-00005-6
10.1242/jcs.264075
10.1007/978-3-030-60204-8_1
10.3389/fphys.2014.00307
10.1242/jcs.146282
10.1073/pnas.1103283108
10.1083/jcb.200601036
10.1016/s0168-9525(00)02056-4
https://doi.org/10.1038/s44320-023-00005-6
https://doi.org/10.1242/jcs.264075
https://doi.org/10.1007/978-3-030-60204-8_1
https://doi.org/10.3389/fphys.2014.00307
https://doi.org/10.1242/jcs.146282
https://doi.org/10.1073/pnas.1103283108
https://doi.org/10.1083/jcb.200601036
https://doi.org/10.1016/s0168-9525(00
https://doi.org/10.1016/S0168-9525(00
https://doi.org/10.1007/s00418-023-02259-5
https://doi.org/10.1083/jcb.200601036,
https://doi.org/10.3389/fphys.2014.00307,
https://doi.org/10.1007/978-3-030-60204-8_1,
https://doi.org/10.1038/s44320-023-00005-6,
https://doi.org/10.3389/fphys.2013.00241,
https://doi.org/10.1242/jcs.146282,
https://doi.org/10.1016/j.jmb.2017.10.009,
https://doi.org/10.1073/pnas.1103283108,
https://doi.org/10.1007/s00418-023-02259-5,
https://doi.org/10.1242/jcs.264075,

📄 View Raw YAML

id: Q9Y5Y5
gene_symbol: PEX16
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  PEX16 is an integral peroxisomal membrane peroxin (peroxin-16) that functions as the
  intra-peroxisomal/ER membrane receptor for PEX3 during peroxisome membrane biogenesis.
  PEX16 is cotranslationally inserted into the ER membrane and traffics to peroxisomes via
  Sec16B-dependent ER export. At the peroxisomal membrane, PEX16 serves as the docking
  receptor for PEX3-PEX19 complexes, enabling the import of peroxisomal membrane proteins
  (PMPs). PEX16 is one of three early peroxins (with PEX3 and PEX19) essential for
  peroxisome membrane assembly; loss of PEX16 leads to complete absence of peroxisomal
  membranes. PEX16 also mediates ER-to-peroxisome trafficking of PMPs including PEX3 and
  PMP34, contributing to both de novo peroxisome formation and ongoing peroxisome maintenance.
  Mutations in PEX16 cause Zellweger spectrum disorders (complementation group 9/CG-D).
alternative_products:
- name: '1'
  id: Q9Y5Y5-1
- name: '2'
  id: Q9Y5Y5-2
  sequence_note: VSP_036593
existing_annotations:
- term:
    id: GO:0007031
    label: peroxisome organization
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      PEX16 is one of three early peroxins (PEX3, PEX16, PEX19) required for peroxisome
      membrane biogenesis in mammals. Loss of PEX16 leads to complete absence of peroxisomes.
      Peroxisome organization is a well-supported core function, though the more specific
      term peroxisome membrane biogenesis (GO:0016557) better captures PEX16's primary role.
      This IBA annotation at the broader level is appropriate and phylogenetically sound.
    action: ACCEPT
    reason: >-
      IBA annotations undergo extensive phylogenetic review and this term accurately captures
      PEX16's role at the appropriate general level. PEX16 is essential for peroxisome
      organization as demonstrated by the complete loss of peroxisomes in PEX16-deficient
      cells (PMID:9837814, PMID:9922452, PMID:16717127).
    supported_by:
    - reference_id: PMID:9837814
      supporting_text: >-
        HsPEX16 expression morphologically and biochemically restored peroxisome biogenesis
        only in fibroblasts from a CG-D patient with ZS
    - reference_id: PMID:9922452
      supporting_text: >-
        expression of PEX16 restores the formation of new peroxisomes in PBD061 cells

- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      PEX16 is an integral peroxisomal membrane protein with two transmembrane helices.
      Both N- and C-terminal domains are exposed to the cytosol. Peroxisomal membrane
      localization is well established by immunofluorescence, cell fractionation, and
      topology studies.
    action: ACCEPT
    reason: >-
      Peroxisomal membrane is the primary functional localization of PEX16, confirmed
      by multiple studies including topology determination (PMID:12223482), immunofluorescence
      (PMID:9837814), and cell fractionation (PMID:9922452). IBA annotation is phylogenetically
      appropriate.
    supported_by:
    - reference_id: PMID:12223482
      supporting_text: >-
        we have determined the membrane topology of Pex16p by differential permeabilization
        method: both N- and C-terminal parts are exposed to the cytosol
    - reference_id: PMID:9837814
      supporting_text: >-
        Pex16p was localized to peroxisomes through expression study of epitope-tagged Pex16p

- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      Combined automated annotation for peroxisomal membrane. Consistent with extensive
      experimental evidence and IBA annotation for the same term.
    action: ACCEPT
    reason: >-
      Redundant with experimentally supported annotations but correct. PEX16 is an
      integral peroxisomal membrane protein.

- term:
    id: GO:0007031
    label: peroxisome organization
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      IEA annotation based on UniProt keyword mapping for peroxisome organization.
      Consistent with IBA and experimental annotations for the same term.
    action: ACCEPT
    reason: >-
      Correct and consistent with extensive experimental evidence. PEX16 is essential
      for peroxisome organization.

- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9603775
  review:
    summary: >-
      Reactome annotation for peroxisomal membrane localization in the context of
      PEX3:PEX19:class I PMP dissociation. PEX16 is located at the peroxisomal
      membrane where PEX3-PEX19-PMP complexes dock.
    action: ACCEPT
    reason: >-
      Correct localization. PEX16 functions at the peroxisomal membrane as the
      receptor for PEX3-PEX19 complexes (PMID:19114594).

- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-NUL-9604086
  review:
    summary: >-
      Reactome annotation for peroxisomal membrane in the context of PEX19:Pex3
      binding PEX16. PEX16 serves as the membrane-anchored receptor at the peroxisomal
      membrane.
    action: ACCEPT
    reason: >-
      Correct localization in context of the PEX3-PEX16 interaction at the peroxisomal
      membrane (PMID:19114594).

- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-NUL-9604116
  review:
    summary: >-
      Reactome annotation for peroxisomal membrane in the context of PEX16:PEX19:Pex3
      dissociation.
    action: ACCEPT
    reason: >-
      Correct localization. Multiple Reactome entries for the same CC term are acceptable
      as they represent different reaction contexts.

- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9603775
  review:
    summary: >-
      Reactome annotation placing PEX16 in the cytosol. However, PEX16 is an integral
      membrane protein that is never found in the cytosol. Cell fractionation shows PEX16
      resides only in the membrane fraction (PMID:16717127). This Reactome annotation
      likely refers to the cytosolic face of PEX16 (both N- and C-termini are cytosolic)
      or to other participants in the reaction, not to PEX16 itself being a cytosolic protein.
    action: REMOVE
    reason: >-
      PEX16 is an integral membrane protein. Kim et al. (2006) showed by cell fractionation
      that PEX16-GFP resided only in the membrane (nonsoluble fraction). PEX16 is never
      cytosolic. This annotation is incorrect for PEX16.
    supported_by:
    - reference_id: PMID:16717127
      supporting_text: >-
        Cell fractionation and immunoblot analysis of PEX16-GFP-transformed COS-7 cells
        performed 24 h after transfection to allow for protein overexpression revealed
        that PEX16-GFP resided only in the membrane (or nonsoluble fraction), in contrast
        to GFP expressed alone, which was primarily in the soluble fraction

- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9603784
  review:
    summary: >-
      Reactome annotation placing PEX16 in cytosol for the PEX19:class I PMP binds PEX3
      reaction. PEX16 is an integral membrane protein and is not cytosolic.
    action: REMOVE
    reason: >-
      PEX16 is never found in the cytosol. It is an integral membrane protein localized
      to peroxisomal membrane and ER membrane (PMID:16717127, PMID:12223482).

- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9603804
  review:
    summary: >-
      Reactome annotation placing PEX16 in cytosol for the PEX19 binds class I PMPs
      reaction. PEX16 is an integral membrane protein and is not cytosolic.
    action: REMOVE
    reason: >-
      PEX16 is never found in the cytosol. It is a multi-pass integral membrane protein
      (PMID:12223482, PMID:16717127). This Reactome-derived annotation is erroneous for PEX16.

- term:
    id: GO:0106101
    label: ER-dependent peroxisome localization
  evidence_type: IDA
  original_reference_id: PMID:19479899
  review:
    summary: >-
      Toro et al. (2009) showed that Pex3p requires Pex16p for ER location and that
      Pex3p-dependent peroxisomal biogenesis initiates in the ER. Cross-expression experiments
      demonstrated that Pex3p requires Pex16p for ER location. This annotation captures
      PEX16's role in ER-dependent peroxisome localization.
    action: ACCEPT
    reason: >-
      Direct evidence from cross-expression experiments showing PEX16's role in
      ER-dependent peroxisome biogenesis. PEX16 localizes to the ER and recruits other
      PMPs there for subsequent transport to peroxisomes.
    supported_by:
    - reference_id: PMID:19479899
      supporting_text: >-
        Cross-expression experiments of Pex3p in GM623 cells lacking Pex16p or Pex16p in
        MR cells lacking Pex3p, showed evidence that Pex3p requires Pex16p for ER
        location but is dispensable for the ER location of Pex16p

- term:
    id: GO:0016020
    label: membrane
  evidence_type: HDA
  original_reference_id: PMID:19946888
  review:
    summary: >-
      High-throughput mass spectrometry study of NK cell membrane proteome identified
      PEX16 in the membrane fraction. The term 'membrane' is very generic; PEX16
      is specifically localized to peroxisomal membrane and ER membrane.
    action: ACCEPT
    reason: >-
      While very generic, this HDA annotation from a proteomics study is not incorrect --
      PEX16 is indeed a membrane protein. More specific terms (peroxisomal membrane,
      ER membrane) are already annotated. This broad term from a large-scale study is
      acceptable as supporting evidence.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19114594
  review:
    summary: >-
      Matsuzaki and Fujiki (2008) demonstrated that PEX16 functions as the membrane
      receptor for PEX3-PEX19 complexes. PEX16 directly binds to PEX3 (shown by
      co-immunoprecipitation of cell-free synthesized proteins) and serves as the
      docking site for PEX3-PEX19 complexes at the peroxisomal membrane.
      The term 'protein binding' is uninformative; a more specific molecular function
      term should be used.
    action: MODIFY
    reason: >-
      While the physical interaction between PEX16 and PEX3 is well established, the
      generic 'protein binding' term is uninformative. PEX16's molecular function is
      better described as acting as a receptor/docking site for PEX3 in the context
      of peroxisome membrane biogenesis. A term like 'protein-membrane targeting activity'
      or 'peroxisomal membrane protein receptor activity' would be more appropriate,
      but no such specific MF term currently exists in GO. The best available alternative
      would be to annotate with GO:0022615 (protein to membrane docking) which is already
      annotated from the same paper.
    proposed_replacement_terms:
    - id: GO:0022615
      label: protein to membrane docking
    supported_by:
    - reference_id: PMID:19114594
      supporting_text: >-
        we demonstrate that Pex16p functions as the Pex3p-docking site and serves as
        the peroxisomal membrane receptor that is specific to the Pex3p-Pex19p complexes

- term:
    id: GO:0022615
    label: protein to membrane docking
  evidence_type: IDA
  original_reference_id: PMID:19114594
  review:
    summary: >-
      Matsuzaki and Fujiki (2008) showed using semi-intact cell import assays and
      co-immunoprecipitation that PEX16 functions as the membrane receptor for PEX3-PEX19
      complexes. Ectopic expression of EGFP-Pex16p specifically enhanced targeting of
      Pex3p to peroxisomes 5-6 fold. Knockdown of Pex16p abrogated Pex3p targeting.
      This term captures PEX16's core molecular function of docking PEX3 at the
      peroxisomal membrane.
    action: ACCEPT
    reason: >-
      This is a core molecular function annotation for PEX16. The paper provides strong
      direct evidence that PEX16 serves as the membrane docking receptor for PEX3-PEX19
      complexes through in vitro import assays, co-IP, and siRNA knockdown experiments.
    supported_by:
    - reference_id: PMID:19114594
      supporting_text: >-
        Pex16p functions as a membrane receptor for Pex3p-Pex19p complexes
    - reference_id: PMID:19114594
      supporting_text: >-
        thereby indicating that Pex16p functions as a receptor for cytosolic
        Pex3p-Pex19p complexes
    - reference_id: PMID:19114594
      supporting_text: >-
        Pex16p was a prerequisite for peroxisomal targeting of newly synthesized Pex3p
        in vivo, functioning as the Pex3p membrane receptor

- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IDA
  original_reference_id: PMID:21768384
  review:
    summary: >-
      Yonekawa et al. (2011) showed PEX16-GFP localizes to peroxisomes and that Sec16B
      regulates the ER-to-peroxisome transport of PEX16. The more specific term
      peroxisomal membrane (GO:0005778) is already annotated with stronger evidence.
    action: ACCEPT
    reason: >-
      Peroxisome localization is correct. While the more specific peroxisomal membrane
      term is preferred and already annotated, this annotation is not wrong.
    supported_by:
    - reference_id: PMID:21768384
      supporting_text: >-
        peroxisomal membrane biogenesis factors peroxin 3 (Pex3) and Pex16 were
        redistributed from peroxisomes to Sec16B-positive ER membranes

- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: IDA
  original_reference_id: PMID:21768384
  review:
    summary: >-
      Yonekawa et al. (2011) demonstrated that PEX16 transits through the ER en route
      to peroxisomes. Knockdown of Sec16B caused redistribution of PEX16-GFP to the ER,
      and overexpression of Sec16B also caused PEX16 redistribution to ER membranes.
      PEX16 ER localization is an intermediate in its trafficking pathway.
    action: ACCEPT
    reason: >-
      PEX16 is found at the ER as an intermediate during its biogenesis and trafficking.
      This is well established by multiple studies.
    supported_by:
    - reference_id: PMID:21768384
      supporting_text: >-
        Knockdown of Sec16B but not Sec16A by RNAi affected the morphology of peroxisomes,
        inhibited the transport of Pex16 from the ER to peroxisomes

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:14709540
  review:
    summary: >-
      Jones et al. (2004) showed PEX19 binds to mPTS regions of PEX16 (amino acids
      221-336 and 59-219). PEX19 functions as a chaperone and import receptor for class 1
      PMPs including PEX16. The interaction is specific and functionally relevant, as PEX19
      controls subcellular distribution of PEX16 mPTS-containing fragments. However,
      'protein binding' is uninformative.
    action: MODIFY
    reason: >-
      The PEX19-PEX16 interaction is real and functionally important, but 'protein binding'
      is uninformative. PEX16 is itself a class 1 PMP that is chaperoned and imported
      by PEX19. The interaction represents PEX16 being a cargo/substrate of PEX19, not
      a specific molecular function of PEX16 itself. Since there is no good GO MF term
      for 'being a substrate of a chaperone', this annotation should be removed in
      favor of the existing BP annotations that capture the functional context.
    proposed_replacement_terms:
    - id: GO:0045046
      label: protein import into peroxisome membrane
    supported_by:
    - reference_id: PMID:14709540
      supporting_text: >-
        PEX19 binds multiple PMP targeting signals
    - reference_id: PMID:14709540
      supporting_text: >-
        Both PMP34aa244-307/3xmyc and PEX16aa221-336/3xmyc were imported into peroxisomes
        in the majority of control cells (88% and 91%, respectively)

- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: HDA
  original_reference_id: PMID:21525035
  review:
    summary: >-
      Bharti et al. (2011) established a procedure for isolating native peroxisomal membrane
      protein complexes from human cells and identified PEX14-associated proteins by mass
      spectrometry. PEX16 was identified as a constituent of peroxisomal membrane complexes,
      confirming its peroxisomal membrane localization.
    action: ACCEPT
    reason: >-
      High-throughput proteomic identification of PEX16 in peroxisomal membrane complexes
      is consistent with extensive experimental evidence for peroxisomal membrane localization.
    supported_by:
    - reference_id: PMID:21525035
      supporting_text: >-
        Using mass spectrometric analysis, almost all known human peroxins involved in
        protein import were identified as constituents of the PEX14 complexes

- term:
    id: GO:0007031
    label: peroxisome organization
  evidence_type: IMP
  original_reference_id: PMID:19479899
  review:
    summary: >-
      Toro et al. (2009) showed using cross-expression experiments in Zellweger syndrome
      cell lines that PEX16 is required for peroxisome biogenesis. Pex3p requires
      Pex16p for ER location during de novo peroxisome formation.
    action: ACCEPT
    reason: >-
      Direct mutant phenotype evidence demonstrates PEX16 is required for peroxisome
      organization. PEX16 is essential for de novo peroxisome biogenesis from the ER.
    supported_by:
    - reference_id: PMID:19479899
      supporting_text: >-
        Cross-expression experiments of Pex3p in GM623 cells lacking Pex16p or Pex16p in
        MR cells lacking Pex3p, showed evidence that Pex3p requires Pex16p for ER
        location but is dispensable for the ER location of Pex16p

- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: IDA
  original_reference_id: PMID:19479899
  review:
    summary: >-
      Toro et al. (2009) showed that PEX16 localizes to the ER when expressed in ZS
      cells lacking PEX3 (MR cells), confirming that PEX16 targets the ER independently
      of PEX3.
    action: ACCEPT
    reason: >-
      ER localization of PEX16 is established as an intermediate in its trafficking pathway,
      particularly during de novo peroxisome formation. PEX16 targets the ER independently
      of PEX3.
    supported_by:
    - reference_id: PMID:19479899
      supporting_text: >-
        Pex3p requires Pex16p for ER location but is dispensable for the ER location of Pex16p

- term:
    id: GO:0032581
    label: ER-dependent peroxisome organization
  evidence_type: IDA
  original_reference_id: PMID:16717127
  review:
    summary: >-
      Kim et al. (2006) provided the first direct evidence in mammalian cells that the ER
      plays a central role in peroxisome biogenesis. They showed PEX16 is cotranslationally
      inserted into the ER and recruits other PMPs to ER membranes, driving de novo
      peroxisome formation. PEX16-GFP with an appended signal anchor sequence could
      complement PEX16-deficient cells, proving the ER pathway is sufficient.
    action: ACCEPT
    reason: >-
      This is a core function annotation. Kim et al. (2006) provided landmark evidence that
      PEX16 regulates ER-dependent peroxisome formation, recruiting PMPs including PEX3
      and PMP34 to ER membranes for subsequent transport to peroxisomes.
    supported_by:
    - reference_id: PMID:16717127
      supporting_text: >-
        We provide direct evidence that peroxisomes can arise de novo from the ER in both
        normal and peroxisome-less mutant cells. We further show that PEX16 regulates
        this process by being cotranslationally inserted into the ER and serving to
        recruit other peroxisomal membrane proteins to membranes.
    - reference_id: PMID:16717127
      supporting_text: >-
        when PEX16-Venus was coexpressed with either PEX3- or PMP34-Cerulean, both PMPs
        colocalized with PEX16-Venus in the ER

- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IDA
  original_reference_id: PMID:9837814
  review:
    summary: >-
      Honsho et al. (1998) showed Pex16p localized to peroxisomes using epitope-tagged
      expression studies. This was the original identification of human PEX16.
    action: ACCEPT
    reason: >-
      Original characterization of human PEX16 showing peroxisomal localization. Well
      supported by subsequent studies.
    supported_by:
    - reference_id: PMID:9837814
      supporting_text: >-
        Pex16p was localized to peroxisomes through expression study of epitope-tagged Pex16p

- term:
    id: GO:0006625
    label: protein targeting to peroxisome
  evidence_type: IMP
  original_reference_id: PMID:9837814
  review:
    summary: >-
      Honsho et al. (1998) showed that PEX16 expression restored peroxisome biogenesis
      in CG-D patient fibroblasts. This encompasses the targeting of peroxisomal proteins
      to the newly formed organelle. While PEX16 is more specifically involved in PMP
      targeting (membrane protein targeting rather than matrix protein targeting), the
      broader term is not incorrect since PEX16 function is prerequisite for all
      peroxisomal protein targeting.
    action: ACCEPT
    reason: >-
      PEX16 is required for peroxisome membrane assembly, which is prerequisite for
      all peroxisomal protein targeting. While PEX16 directly mediates PMP import rather
      than matrix protein import, loss of PEX16 abolishes all protein targeting to
      peroxisomes because no peroxisomes exist.
    supported_by:
    - reference_id: PMID:9837814
      supporting_text: >-
        HsPEX16 expression morphologically and biochemically restored peroxisome biogenesis
        only in fibroblasts from a CG-D patient with ZS

- term:
    id: GO:0016557
    label: peroxisome membrane biogenesis
  evidence_type: IMP
  original_reference_id: PMID:9837814
  review:
    summary: >-
      Honsho et al. (1998) demonstrated that mutation in PEX16 causes loss of peroxisomes
      in CG-D/CG-IX Zellweger syndrome. Introduction of wild-type PEX16 restores
      peroxisome biogenesis. This is the most specific and accurate core function
      annotation for PEX16.
    action: ACCEPT
    reason: >-
      Peroxisome membrane biogenesis is the primary biological process function of PEX16.
      Patient cells with PEX16 mutations completely lack peroxisomal membranes, and
      complementation restores them.
    supported_by:
    - reference_id: PMID:9837814
      supporting_text: >-
        HsPEX16 expression morphologically and biochemically restored peroxisome biogenesis
        only in fibroblasts from a CG-D patient with ZS

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15713480
  review:
    summary: >-
      Fransen et al. (2005) performed pentapeptide scanning mutagenesis of PEX19 and
      identified that PEX19's carboxy-terminal domain interacts with multiple PMPs
      including PEX16. This paper is primarily about PEX19's domain structure, and PEX16
      is one of many PMPs tested as a binding partner. The 'protein binding' annotation
      is uninformative.
    action: MODIFY
    reason: >-
      Generic protein binding is uninformative. The interaction documented is PEX19
      binding PEX16 as a cargo/substrate for chaperoning and import. This is the same
      interaction documented in PMID:14709540. Should be replaced with a more specific
      annotation or removed as redundant.
    proposed_replacement_terms:
    - id: GO:0045046
      label: protein import into peroxisome membrane
    supported_by:
    - reference_id: PMID:15713480
      supporting_text: >-
        a carboxy-terminal domain that interacts with multiple PMPs including Pex3p,
        Pex11pbeta, Pex12p, Pex13p, Pex16p, and Pex26p

- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: IDA
  original_reference_id: PMID:16717127
  review:
    summary: >-
      Kim et al. (2006) showed by fluorescence microscopy and cell fractionation that
      PEX16-GFP localizes to ER membranes in addition to peroxisomes. In cells lacking
      peroxisomes (PBD399-T1 or PBD400), PEX16-GFP was exclusively in the ER. In vitro
      assays confirmed cotranslational insertion into ER microsomes. FLIP experiments
      showed PEX16-GFP diffuses freely throughout the ER.
    action: ACCEPT
    reason: >-
      ER membrane is a bona fide localization of PEX16, representing the site of its
      cotranslational insertion and a transit point during trafficking to peroxisomes.
      Strong experimental evidence from imaging, fractionation, and in vitro insertion assays.
    supported_by:
    - reference_id: PMID:16717127
      supporting_text: >-
        The distribution of PEX16-GFP in these cells included the ER as well as peroxisomes
    - reference_id: PMID:16717127
      supporting_text: >-
        a significant proportion of PEX16-glyc molecules underwent glycosylation during
        cotranslational targeting, whereas none did so during posttranslational targeting.
        The data thus confirmed that PEX16 undergoes cotranslational insertion into the ER

- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: IDA
  original_reference_id: PMID:12223482
  review:
    summary: >-
      Honsho et al. (2002) determined the membrane topology of PEX16 by differential
      permeabilization, showing it is an integral peroxisomal membrane protein with
      both N- and C-terminal domains exposed to the cytosol. They identified the
      topogenic sequence (residues 66-81 and the first transmembrane segment) essential
      for membrane integration.
    action: ACCEPT
    reason: >-
      Direct experimental evidence for peroxisomal membrane localization and topology
      determination. This is a primary characterization study.
    supported_by:
    - reference_id: PMID:12223482
      supporting_text: >-
        we have determined the membrane topology of Pex16p by differential permeabilization
        method: both N- and C-terminal parts are exposed to the cytosol

- term:
    id: GO:0016557
    label: peroxisome membrane biogenesis
  evidence_type: IMP
  original_reference_id: PMID:12223482
  review:
    summary: >-
      Honsho et al. (2002) showed that overexpression of dysfunctional PEX16 variants
      interfered with peroxisome membrane assembly. The C-terminal cytoplasmic part of
      PEX16 abrogated peroxisome restoration in pex3 mutants, implying PEX16 functions
      upstream of PEX3 in peroxisome membrane assembly.
    action: ACCEPT
    reason: >-
      Functional evidence that PEX16 is required for peroxisome membrane biogenesis,
      acting upstream of PEX3 in the pathway.
    supported_by:
    - reference_id: PMID:12223482
      supporting_text: >-
        Pex16p C-terminal cytoplasmic part severely abrogated peroxisome restoration in
        pex mutants such as matrix protein import-defective pex12 and membrane assembly
        impaired pex3 by respective PEX12 and PEX3 expression

- term:
    id: GO:0045046
    label: protein import into peroxisome membrane
  evidence_type: IMP
  original_reference_id: PMID:12223482
  review:
    summary: >-
      Honsho et al. (2002) showed that dysfunctional PEX16 variants interfered with
      localization of PMPs (Pex14p, Pex13p, PMP70) to peroxisomes, demonstrating that
      PEX16 is required for PMP import into the peroxisome membrane.
    action: ACCEPT
    reason: >-
      Direct evidence that PEX16 function is required for import of PMPs (Pex14p, Pex13p,
      PMP70) into the peroxisome membrane. This is a core function annotation.
    supported_by:
    - reference_id: PMID:12223482
      supporting_text: >-
        Localization to peroxisomes of membrane proteins such as Pex14p, Pex13p, and PMP70
        was interfered with in CHO-K1 cells by a higher level expression of the pex16
        patient-derived dysfunctional but topogenically active Pex16pR176ter

- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IDA
  original_reference_id: PMID:15813749
  review:
    summary: >-
      Brocard et al. (2005) used PEX16-mutant cells for microinjection complementation
      studies examining microtubule requirements for peroxisome biogenesis. PEX16 was
      expressed and localized to newly formed peroxisomes in complemented cells.
    action: ACCEPT
    reason: >-
      Peroxisome localization of PEX16 confirmed in the context of complementation experiments.
    supported_by:
    - reference_id: PMID:15813749
      supporting_text: >-
        nuclear microinjection of plasmids expressing EGFP-SKL and Pex16p in PEX16-mutant
        cells resulted in the accumulation of EGFP-SKL into newly formed peroxisomes

- term:
    id: GO:0007031
    label: peroxisome organization
  evidence_type: IMP
  original_reference_id: PMID:15813749
  review:
    summary: >-
      Brocard et al. (2005) showed that PEX16 complementation in PEX16-mutant cells
      restores peroxisome formation, and that this process requires microtubules and
      dynein motors. This demonstrates PEX16's role in peroxisome organization.
    action: ACCEPT
    reason: >-
      Complementation of PEX16-mutant cells demonstrates PEX16 is required for
      peroxisome organization. The paper adds mechanistic context (microtubule dependence).
    supported_by:
    - reference_id: PMID:15813749
      supporting_text: >-
        pretreatment of the cells with nocodazol, prior to microinjection, resulted in
        the inhibition of complementation of the PEX16 mutant

- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: IMP
  original_reference_id: PMID:9922452
  review:
    summary: >-
      South and Gould (1999) showed that PBD061 cells (PEX16-deficient) lack detectable
      peroxisome membranes and cannot import PMPs. Expression of PEX16 restores peroxisome
      membranes. This demonstrates PEX16 is required for peroxisomal membrane formation.
      However, the evidence type IMP with CC term is unusual -- this represents the
      mutant phenotype showing PEX16 is required for peroxisomal membrane existence.
    action: ACCEPT
    reason: >-
      Mutant phenotype demonstrates PEX16 is essential for peroxisomal membrane formation.
      PEX16-deficient cells completely lack peroxisomal membranes.
    supported_by:
    - reference_id: PMID:9922452
      supporting_text: >-
        we report here a Zellweger syndrome patient (PBD061) with an unusual cellular
        phenotype, an inability to import peroxisomal membrane proteins
    - reference_id: PMID:9922452
      supporting_text: >-
        expression of PEX16 restores the formation of new peroxisomes in PBD061 cells

- term:
    id: GO:0016558
    label: protein import into peroxisome matrix
  evidence_type: IMP
  original_reference_id: PMID:9922452
  review:
    summary: >-
      South and Gould (1999) showed that PBD061 (PEX16-deficient) cells are unable to
      import peroxisomal matrix proteins because they lack peroxisomes entirely. After
      PEX16 complementation, matrix protein import was restored following membrane
      assembly. However, PEX16 is not directly involved in matrix protein import -- it
      is required for membrane biogenesis, which is prerequisite for matrix import.
      This annotation conflates an indirect downstream effect with a direct function.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      PEX16 is not directly involved in peroxisome matrix protein import. Its role is
      in membrane biogenesis. The inability to import matrix proteins in PEX16-deficient
      cells is an indirect consequence of having no peroxisomal membranes. The direct
      function is peroxisome membrane biogenesis (GO:0016557), which is already annotated.
      South and Gould (1999) themselves noted: "Peroxisome synthesis and peroxisomal
      membrane protein import could be detected within 2-3 h of PEX16 injection and
      was followed by matrix protein import" -- showing matrix import is a downstream
      consequence, not a direct PEX16 function.
    supported_by:
    - reference_id: PMID:9922452
      supporting_text: >-
        Peroxisome synthesis and peroxisomal membrane protein import could be detected
        within 2-3 h of PEX16 injection and was followed by matrix protein import

- term:
    id: GO:0060090
    label: molecular adaptor activity
  evidence_type: IDA
  original_reference_id: PMID:19114594
  review:
    summary: >-
      PEX16 functions as a molecular adaptor/receptor at the peroxisomal membrane,
      bringing together PEX3 and PEX19 in a trimeric complex to enable PMP delivery.
      Matsuzaki and Fujiki (2008) demonstrated that PEX16 is the membrane receptor
      for PEX3-PEX19 complexes using semi-intact cell import assays. Lee et al. (2024)
      confirmed a specific PEX3-PEX16 interface (PEX16 loop residues 132-214) with
      PEX19 binding PEX3 on the opposite face, supporting a trimeric adaptor model.
      This MF term is not currently annotated in GOA but accurately describes
      PEX16's core molecular function of bridging PEX3 and PEX19 at the membrane.
    action: NEW
    reason: >-
      PEX16 acts as a molecular adaptor by bringing together PEX3 (via direct binding
      through its cytosolic loop) and PEX19 (indirectly, through the PEX3-PEX19 interaction)
      at the peroxisomal membrane. This adaptor/scaffold function is the core molecular
      activity of PEX16. The existing 'protein binding' annotations are uninformative,
      and 'protein to membrane docking' (GO:0022615) is a BP term. GO:0060090 (molecular
      adaptor activity) best captures PEX16's role as a membrane-anchored receptor that
      coordinates the PEX3-PEX16-PEX19 assembly for PMP delivery.
    supported_by:
    - reference_id: PMID:19114594
      supporting_text: >-
        we demonstrate that Pex16p functions as the Pex3p-docking site and serves as
        the peroxisomal membrane receptor that is specific to the Pex3p-Pex19p complexes
    - reference_id: PMID:19114594
      supporting_text: >-
        Pex16p was a prerequisite for peroxisomal targeting of newly synthesized Pex3p
        in vivo, functioning as the Pex3p membrane receptor
references:
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:12223482
  title: The membrane biogenesis peroxin Pex16p. Topogenesis and functional roles
    in peroxisomal membrane assembly.
  findings:
  - statement: PEX16 membrane topology determined -- both N and C termini cytosolic, two transmembrane segments
  - statement: Residues 66-81 and first TM segment required for peroxisomal membrane integration
  - statement: Dysfunctional PEX16 variants interfere with PMP localization (Pex14p, Pex13p, PMP70)
  - statement: PEX16 C-terminal domain abrogates peroxisome restoration in pex3 and pex12 mutants
- id: PMID:14709540
  title: PEX19 is a predominantly cytosolic chaperone and import receptor for class
    1 peroxisomal membrane proteins.
  findings:
  - statement: PEX19 binds and stabilizes newly synthesized PMPs including PEX16 in the cytosol
  - statement: PEX16 contains two mPTS regions bound by PEX19 (aa 59-219 and aa 221-336)
  - statement: PEX19 functions as both chaperone and import receptor for class 1 PMPs
  - statement: Inhibition of PEX19 causes specific PMP import defect
- id: PMID:15713480
  title: Analysis of human Pex19p's domain structure by pentapeptide scanning mutagenesis.
  findings:
  - statement: PEX19 carboxy-terminal domain interacts with PEX16 among other PMPs
  - statement: PEX19 has tripartite domain structure with PEX3-binding, PEX14-binding, and PMP-binding domains
- id: PMID:15813749
  title: Requirement for microtubules and dynein motors in the earliest stages of
    peroxisome biogenesis.
  findings:
  - statement: PEX16 complementation of mutant cells requires microtubules and dynein motors
  - statement: Nocodazol and dominant-negative dynactin prevent PEX16-mediated peroxisome restoration
- id: PMID:16717127
  title: The origin and maintenance of mammalian peroxisomes involves a de novo PEX16-dependent
    pathway from the ER.
  findings:
  - statement: PEX16 is cotranslationally inserted into the ER
  - statement: PEX16 traffics from ER to peroxisomes (photoactivation pulse-chase)
  - statement: PEX16 recruits PEX3 and PMP34 to ER membranes
  - statement: PEX16 with signal anchor sequence complements PEX16-deficient cells from ER
  - statement: New peroxisomes derive primarily from ER in growing cells
- id: PMID:19114594
  title: The peroxisomal membrane protein import receptor Pex3p is directly transported
    to peroxisomes by a novel Pex19p- and Pex16p-dependent pathway.
  findings:
  - statement: PEX16 functions as the membrane receptor for PEX3-PEX19 complexes
  - statement: Ectopic PEX16 expression enhances PEX3 targeting 5-6 fold
  - statement: PEX16 knockdown abrogates PEX3 peroxisomal targeting
  - statement: PEX3 mPTS directly binds PEX16 (co-IP of cell-free synthesized proteins)
  - statement: Both N- and C-terminal regions of PEX16 indispensable for recruiting PEX3-PEX19 complexes
- id: PMID:19479899
  title: Pex3p-dependent peroxisomal biogenesis initiates in the endoplasmic reticulum
    of human fibroblasts.
  findings:
  - statement: Pex3p requires Pex16p for ER location but not vice versa
  - statement: Pex3p follows ER-to-peroxisome route in mammalian cells
  - statement: De novo peroxisome biogenesis involves ER intermediate
- id: PMID:19946888
  title: Defining the membrane proteome of NK cells.
  findings:
  - statement: Large-scale proteomics study identifying PEX16 in membrane fraction of NK cells
- id: PMID:21525035
  title: PEX14 is required for microtubule-based peroxisome motility in human cells.
  findings:
  - statement: PEX16 identified as peroxisomal membrane protein by mass spectrometry in PEX14 complex isolation
- id: PMID:21768384
  title: Sec16B is involved in the endoplasmic reticulum export of the peroxisomal
    membrane biogenesis factor peroxin 16 (Pex16) in mammalian cells.
  findings:
  - statement: Sec16B required for ER-to-peroxisome transport of PEX16
  - statement: Sec16B knockdown causes PEX16 redistribution to ER and peroxisome elongation
  - statement: PEX16 Sec16B-dependent trafficking links ER exit site machinery to peroxisome biogenesis
- id: PMID:9837814
  title: Mutation in PEX16 is causal in the peroxisome-deficient Zellweger syndrome
    of complementation group D.
  findings:
  - statement: PEX16 identified as causative gene for CG-D (CG-IX) Zellweger syndrome
  - statement: PEX16 encodes 336 amino acid peroxisomal protein
  - statement: R176ter nonsense mutation found in patient
  - statement: PEX16 expression restores peroxisome biogenesis in CG-D patient fibroblasts
- id: PMID:9922452
  title: Peroxisome synthesis in the absence of preexisting peroxisomes.
  findings:
  - statement: PBD061 cells (PEX16-deficient) lack peroxisomal membranes and cannot import PMPs
  - statement: PEX16 expression restores peroxisome formation de novo
  - statement: PMP import precedes matrix protein import after PEX16 complementation
  - statement: Peroxisomes can form without preexisting peroxisomes
- id: Reactome:R-HSA-9603775
  title: PEX3:PEX19:class I PMP dissociates
  findings: []
- id: Reactome:R-HSA-9603784
  title: PEX19:class I PMP binds PEX3
  findings: []
- id: Reactome:R-HSA-9603804
  title: PEX19 binds class I peroxisomal membrane proteins
  findings: []
- id: Reactome:R-NUL-9604086
  title: PEX19:Pex3 binds PEX16
  findings: []
- id: Reactome:R-NUL-9604116
  title: PEX16:PEX19:Pex3 dissociates
  findings: []
core_functions:
- molecular_function:
    id: GO:0060090
    label: molecular adaptor activity
  description: >-
    PEX16 is an integral peroxisomal membrane peroxin that functions as the membrane
    receptor/docking site for PEX3-PEX19 complexes. PEX16 binds PEX3 directly via a
    cytosolic loop (residues 132-214) and enables PMP delivery to the peroxisomal
    membrane. PEX16 is essential for peroxisome membrane biogenesis; loss of PEX16
    leads to complete absence of peroxisomal membranes and causes Zellweger spectrum
    disorders (complementation group 9). PEX16 also mediates ER-dependent de novo
    peroxisome formation by being cotranslationally inserted into the ER and recruiting
    other PMPs (PEX3, PMP34) to ER membranes for subsequent transport to peroxisomes.
  directly_involved_in:
  - id: GO:0016557
    label: peroxisome membrane biogenesis
  - id: GO:0032581
    label: ER-dependent peroxisome organization
  - id: GO:0045046
    label: protein import into peroxisome membrane
  - id: GO:0007031
    label: peroxisome organization
  locations:
  - id: GO:0005778
    label: peroxisomal membrane
  - id: GO:0005789
    label: endoplasmic reticulum membrane
  supported_by:
  - reference_id: PMID:19114594
    supporting_text: >-
      we demonstrate that Pex16p functions as the Pex3p-docking site and serves as
      the peroxisomal membrane receptor that is specific to the Pex3p-Pex19p complexes
  - reference_id: PMID:16717127
    supporting_text: >-
      We provide direct evidence that peroxisomes can arise de novo from the ER in both
      normal and peroxisome-less mutant cells. We further show that PEX16 regulates
      this process by being cotranslationally inserted into the ER and serving to
      recruit other peroxisomal membrane proteins to membranes.
  - reference_id: PMID:9837814
    supporting_text: >-
      HsPEX16 expression morphologically and biochemically restored peroxisome biogenesis
      only in fibroblasts from a CG-D patient with ZS

PEX16

Gene Description

Existing Annotations Review

Core Functions

References

Deep Research

Falcon

Research Report: Human PEX16 (UniProt Q9Y5Y5) — Functional Annotation, Mechanism, and Disease Relevance

0) Target verification (critical identity check)

1) Key concepts and definitions (current understanding)

1.1 Peroxisome biogenesis and “early peroxins”

1.2 Molecular function of PEX16 (functional definition)

2) Subcellular localization and trafficking routes

2.1 ER-to-peroxisome route for PEX16 and PMP delivery

2.2 PEX16 in peroxisome maintenance via ER trafficking

2.3 ER export machinery involvement (Sec16B)

3) Interaction partners and molecular assembly (PEX3–PEX19–PEX16)

3.1 Canonical module: PEX19 (cytosolic carrier) → PEX3/PEX16 (membrane receptors)

3.2 2024 structural/interface advance: validated PEX3–PEX16 interface and trimer model

4) Recent developments and latest research (prioritizing 2023–2024)

4.1 Variant interpretation and mechanistic clarity via interface mapping (2024)

4.2 2024 review context: peroxisome biology as an active frontier

5) Disease relevance: Zellweger spectrum / peroxisome biogenesis disorders (PBDs)

5.1 PEX16 is a PBD gene (Complementation Group 9)

5.2 Cellular phenotypes in PEX16-deficient patient cells and rescue

6) Current applications and real-world implementations

6.1 Clinical genetics: diagnosis and classification

6.2 Variant interpretation and mechanistic annotation

6.3 Cell biology toolkits and model systems

7) Expert synthesis and analysis (authoritative perspectives)

7.1 Consensus vs evolving points

7.2 Mechanistic refinement with structural models (2024)

8) Key statistics and quantitative data points (from available sources)

9) Evidence figure

Embedded evidence table (key papers, dates, URLs)

References (URLs and publication dates)

Citations

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