SlyD

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0003755 peptidyl-prolyl cis-trans isomerase activity	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for PPIase activity. SlyD is an FKBP-type PPIase with demonstrated catalytic activity for the cis-trans isomerization of Xaa-Pro bonds (PMID:9188461, PMID:16388577). The PPIase activity is carried in the N-terminal FKBP domain and is conserved across SlyD orthologs. Reason: PPIase activity is one of SlyD's two primary enzymatic activities and is well-supported by both phylogenetic inference and direct experimental evidence (PMID:9188461, PMID:16388577). Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN005358675 · PANTHER:PTN005358675 SUPPORTS TRANSFER Current PTHR47861 PAINT retains PPIase activity at this ancestral node. UniProtKB:P0A9K9 · UniProtKB:P0A9K9 SUPPORTS TRANSFER SlyD itself provides direct descendant evidence for PPIase activity; its presence in the IBA trace is expected and is not circular. Supporting Evidence: PMID:9188461 For Suc-Ala-Phe-Pro-Arg-4-nitroanilide as substrate, kcat/Km of 29,600 M-1 s-1 for SlyD and 18,600 M-1 s-1 for the N-terminal fragment were obtained. file:ECOLI/SlyD/SlyD-deep-research-falcon.md The literature summarized here consistently describes *SlyD in Escherichia coli* as (i) an FKBP-type peptidyl‑prolyl cis/trans isomerase (PPIase; EC 5.2.1.8)**
GO:0005829 cytosol	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for cytosol localization. Consistent with IDA evidence from proteomics studies (PMID:15911532, PMID:18304323) and UniProt subcellular location annotation. Reason: Cytosol localization is well-established for SlyD by both phylogenetic inference and proteomics-based experimental evidence. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN005358675 · PANTHER:PTN005358675 SUPPORTS TRANSFER Current PTHR47861 PAINT retains cytosol localization at this ancestral node. UniProtKB:P0A9K9 · UniProtKB:P0A9K9 SUPPORTS TRANSFER SlyD's experimental cytosol annotation validly seeds the ancestral assertion; target self-seeding is expected and not circular.
GO:0042026 protein refolding	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for protein refolding. SlyD has both PPIase and chaperone activities that together promote protein folding and refolding (PMID:16388577, PMID:19356587). The PPIase catalyzes proline-limited refolding steps while the IF domain prevents aggregation of folding intermediates. Reason: SlyD's combined PPIase and chaperone activities make it a bona fide folding helper protein. The protein refolding function is conserved across the SlyD family (PMID:16388577) and supported by IDA evidence. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN005358675 · PANTHER:PTN005358675 SUPPORTS TRANSFER Current PTHR47861 PAINT retains protein refolding at this ancestral node. UniProtKB:P0A9K9 · UniProtKB:P0A9K9 SUPPORTS TRANSFER SlyD itself has direct refolding evidence, so its appearance among the descendant seeds is valid experimental grounding rather than circularity. Supporting Evidence: PMID:16388577 All SlyD variants catalyze the proline-limited refolding of ribonuclease T1 with very high efficiencies, and the specificity constants (kcat/KM) are equal to approximately 10(6) M(-1) s(-1).
GO:0003755 peptidyl-prolyl cis-trans isomerase activity	IEA GO_REF:0000120	ACCEPT	Summary: IEA annotation for PPIase activity from combined automated methods. Consistent with the IBA and IDA annotations for the same term. Reason: PPIase activity is a core function supported by multiple evidence types. This broader IEA annotation is acceptable.
GO:0005737 cytoplasm	IEA GO_REF:0000044	ACCEPT	Summary: IEA annotation for cytoplasm localization from UniProt subcellular location mapping. Broader parent of cytosol. UniProt confirms cytoplasmic localization. Reason: Cytoplasmic localization is correct and well-established. The more specific cytosol term is annotated with IDA and IBA evidence.
GO:0042026 protein refolding	IEA GO_REF:0000117	ACCEPT	Summary: IEA annotation for protein refolding from ARBA machine learning models. Consistent with the IBA and IDA annotations for the same term. Reason: Protein refolding is a well-supported function. This IEA annotation is consistent with stronger evidence types.
GO:0005515 protein binding	IPI PMID:15690043 Interaction network containing conserved and essential prote...	UNDECIDED	Summary: High-throughput IPI evidence for association of SlyD with HypB. Reason: Like the GrcA row from this high-throughput experiment, this row establishes physical association only and does not resolve functional directionality. Separate pathway-focused studies show that HypB releases nickel to SlyD, so the interaction must not be promoted to SlyD-mediated delivery to a target protein.
GO:0005515 protein binding	IPI PMID:15690043 Interaction network containing conserved and essential prote...	UNDECIDED	Summary: High-throughput IPI evidence for association of SlyD with GrcA. Reason: The cached high-throughput study does not establish a SlyD-specific functional context for the GrcA interaction. With no full assay-level evidence available, curator deference requires retaining the record without assigning it to nickel chaperoning.
GO:0005515 protein binding	IPI PMID:16412426 Interactions of the Escherichia coli hydrogenase biosyntheti...	KEEP AS NON CORE	Summary: IPI annotation for SlyD-HypB complex formation in a study of E. coli hydrogenase biosynthetic proteins. Reason: The SlyD-HypB interaction is biologically meaningful within hydrogenase maturation, but HypB is the upstream nickel donor to SlyD rather than SlyD's delivery target. No more informative molecular-function replacement is justified from this IPI row alone.
GO:0005515 protein binding	IPI PMID:19402753 Global functional atlas of Escherichia coli encompassing pre...	UNDECIDED	Summary: Global interaction-atlas IPI evidence for association of SlyD with HypB. Reason: Like the GrcA row from the same interaction atlas, this high-throughput association does not establish a SlyD-specific molecular activity or its direction. It therefore cannot be promoted to nickel chaperone activity.
GO:0005515 protein binding	IPI PMID:19402753 Global functional atlas of Escherichia coli encompassing pre...	UNDECIDED	Summary: Global interaction-atlas IPI evidence for association of SlyD with GrcA. Reason: The cached full interaction atlas does not establish a specific biological role for the SlyD-GrcA association. It cannot be reassigned to nickel chaperone activity merely because a separate row from the same paper names HypB.
GO:0005515 protein binding	IPI PMID:21185288 The Escherichia coli metal-binding chaperone SlyD interacts ...	KEEP AS NON CORE	Summary: IPI evidence for association of SlyD with the nickel-incorporation factor HypB during hydrogenase 3 maturation. Reason: The interaction is pathway-specific, but HypB donates nickel to SlyD and is not the target to which SlyD delivers nickel. Retain the physical interaction as non-core without using it as a directional nickel-chaperone replacement.
GO:0005515 protein binding	IPI PMID:21185288 The Escherichia coli metal-binding chaperone SlyD interacts ...	MODIFY	Summary: IPI evidence for a direct SlyD-HycE association during hydrogenase 3 metallocenter assembly. Reason: The interaction precedes metal insertion and is mediated by SlyD's chaperone domain. In synthesis with the nickel-specific physiological evidence, GO:0170061 captures the functional activity without claiming that this IPI alone visualized nickel transfer. Proposed replacements: nickel chaperone activity Supporting Evidence: PMID:21185288 A SlyD-HycE interaction preceding both iron and nickel insertion to the enzyme was detected, mediated by the chaperone domain of SlyD, and independent of HypB.
GO:0005515 protein binding	IPI PMID:21185288 The Escherichia coli metal-binding chaperone SlyD interacts ...	MODIFY	Summary: EcoCyc independently retains the experimentally supported SlyD-HycE IPI assertion from this hydrogenase 3 maturation study. Reason: This physical interaction is functionally interpreted with the nickel-specific maturation evidence as GO:0170061; the duplicate source record is preserved to maintain physical GOA row parity. Proposed replacements: nickel chaperone activity Supporting Evidence: PMID:21185288 A SlyD-HycE interaction preceding both iron and nickel insertion to the enzyme was detected, mediated by the chaperone domain of SlyD, and independent of HypB.
GO:0005515 protein binding	IPI PMID:22016389 Protein interactions and localization of the Escherichia col...	MODIFY	Summary: IPI annotation from Chan Chung and Zamble (2011) showing SlyD interaction with HycE (P16431) during nickel insertion to [NiFe] hydrogenase. Reason: Interaction with HycE is in the context of nickel delivery during hydrogenase maturation. GO:0170061 "nickel chaperone activity" is more informative. Proposed replacements: nickel chaperone activity
GO:0000413 protein peptidyl-prolyl isomerization	IDA PMID:9188461 The Escherichia coli SlyD is a metal ion-regulated peptidyl-...	ACCEPT	Summary: IDA annotation for protein peptidyl-prolyl isomerization from Hottenrott et al. (1997). SlyD was demonstrated to catalyze cis/trans isomerization of peptidyl-prolyl bonds with kcat/Km of 29,600 M-1 s-1 for Suc-Ala-Phe-Pro-Arg-4-nitroanilide. The PPIase activity is reversibly inhibited by Ni2+ binding to the C-terminal histidine-rich region. Reason: Direct experimental evidence for the biological process of peptidyl-prolyl isomerization. This is one of SlyD's core catalytic activities. Supporting Evidence: PMID:9188461 the PPIase activity of SlyD is reversibly regulated by binding of three Ni2+ ions to the histidine-rich, C-terminal region
GO:0042026 protein refolding	IDA PMID:16388577 SlyD proteins from different species exhibit high prolyl iso...	ACCEPT	Summary: IDA annotation for protein refolding from Scholz et al. (2006). The study demonstrated that SlyD proteins from multiple species catalyze proline-limited refolding of ribonuclease T1 with very high efficiency and also exhibit pronounced chaperone properties that prevent aggregation. Reason: Strong experimental evidence for SlyD's role in protein refolding. SlyD combines PPIase and chaperone activities that together promote efficient protein folding, making it a bona fide folding helper protein. Supporting Evidence: PMID:16388577 SlyD also exhibits pronounced chaperone properties. Permanently unfolded proteins bind with high affinity to SlyD and thus inhibit its prolyl isomerase activity.
GO:0051604 protein maturation	IMP PMID:17426034 The role of complex formation between the Escherichia coli h...	ACCEPT	Summary: IMP annotation for protein maturation from Leach et al. (2007). Mutations in SlyD that disrupt complex formation with HypB result in deficient hydrogenase production in vivo. SlyD stimulates release of nickel from HypB's high-affinity Ni(II)-binding site, and a SlyD truncation lacking the C-terminal metal-binding tail is not functional in vivo for hydrogenase maturation. Reason: Well-supported by mutant phenotype evidence. SlyD is required for proper maturation of the [NiFe]-hydrogenase metallocenter. This is a core in vivo function. Supporting Evidence: PMID:17426034 Mutations in either protein that disrupt complex formation in vitro also result in deficient hydrogenase production in vivo, indicating that the contact between HypB and SlyD is important for hydrogenase maturation.
GO:0005515 protein binding	IPI PMID:30758762 Complex formation between the Escherichia coli [NiFe]-hydrog...	KEEP AS NON CORE	Summary: IPI annotation from Khorasani-Motlagh et al. (2019) showing SlyD-HypB complex formation with KD of 24 nM. SlyD blocks HypA-HypB interaction. Reason: This directly measured complex is relevant to nickel maturation, but HypB is the upstream nickel donor to SlyD rather than SlyD's delivery target. The IPI evidence is retained as a non-core interaction without a directional MF replacement. Supporting Evidence: PMID:30758762 The affinity of HypB-SlyD was measured by using surface plasmon resonance, which revealed a KD of 24 ± 10 nM in the absence of nucleotide and an interaction several fold tighter in the presence of GDP
GO:0005515 protein binding	IPI PMID:32813023 YdiV regulates Escherichia coli ferric uptake by manipulatin...	KEEP AS NON CORE	Summary: IPI annotation for protein binding from Zhang et al. (2020) showing SlyD interaction with Fur (P0A9A9) in the YdiV-SlyD-Fur regulatory pathway for iron homeostasis. SlyD's PPIase activity transforms Fur into a form that does not bind DNA under iron deficiency conditions. Reason: This is a genuine protein-protein interaction, but in a non-core context (iron homeostasis regulation via YdiV-SlyD-Fur pathway). The "protein binding" term is vague, but this interaction represents a secondary regulatory role of SlyD rather than its primary functions. The interaction is biologically meaningful but peripheral to SlyD's core PPIase/chaperone/metallochaperone functions. Supporting Evidence: PMID:32813023 High levels of YdiV then transforms Fur into a novel form which does not bind DNA in a peptidyl-prolyl cis-trans isomerase SlyD dependent manner.
GO:0005829 cytosol	IDA PMID:15911532 Localization, annotation, and comparison of the Escherichia ...	ACCEPT	Summary: IDA annotation for cytosol localization from the proteomics study by Lopez-Campistrous et al. (2005). Reason: Proteomics-based experimental evidence for cytosol localization.
GO:0005829 cytosol	IDA PMID:18304323 Protein abundance profiling of the Escherichia coli cytosol.	ACCEPT	Summary: IDA annotation for cytosol localization from proteomics study by Ishihama et al. (2008). Reason: The paper reports a large-scale cytosolic proteome rather than discussing SlyD individually in the abstract. The experimental curator had access to the protein-level dataset, so this annotation is retained with that scope made explicit. Supporting Evidence: PMID:18304323 we identified 1103 proteins from the cytosolic fraction of the Escherichia coli strain MC4100.
GO:0005507 copper ion binding	IDA PMID:22047179 Metal selectivity of the Escherichia coli nickel metallochap...	KEEP AS NON CORE	Summary: IDA annotation for copper ion binding from Kaluarachchi et al. (2011). The C-terminal domain of SlyD binds Cu(I) with the highest affinity among all metals tested. However, in vivo, SlyD has a Ni(II)-specific function. Reason: Copper binding is experimentally demonstrated in vitro (PMID:22047179), but the in vivo function of SlyD is specifically as a nickel metallochaperone. The copper binding may not be physiologically relevant, as the same study notes "in vivo studies reveal a Ni(II)-specific function for the protein." Supporting Evidence: PMID:22047179 Although the purified protein is unable to overcome the large thermodynamic preference for Cu(I) and exclude Zn(II) chelation in the presence of Ni(II), in vivo studies reveal a Ni(II)-specific function for the protein.
GO:0008270 zinc ion binding	IDA PMID:22047179 Metal selectivity of the Escherichia coli nickel metallochap...	KEEP AS NON CORE	Summary: IDA annotation for zinc ion binding from Kaluarachchi et al. (2011). SlyD binds zinc with affinity similar to nickel in vitro, but in vivo function is nickel-specific. Reason: Zinc binding is experimentally demonstrated (PMID:22047179, PMID:8300624), but SlyD's in vivo metallochaperone function is specific to nickel. Zinc binding may represent a property of the metal-binding domain rather than a specific biological function. Supporting Evidence: PMID:22047179 The order of affinities of SlyD for the metals examined is as follows: Mn(II) and Fe(II) < Co(II) < Ni(II) ~ Zn(II) ≪ Cu(I)
GO:0016151 nickel cation binding	IDA PMID:22047179 Metal selectivity of the Escherichia coli nickel metallochap...	ACCEPT	Summary: IDA annotation for nickel cation binding from Kaluarachchi et al. (2011). SlyD binds multiple Ni(II) ions with submicromolar affinity in the C-terminal domain. Reason: Nickel binding is the physiologically relevant metal-binding function of SlyD, directly related to its role as a nickel metallochaperone for [NiFe]-hydrogenase maturation (PMID:22047179, PMID:19947632). Supporting Evidence: PMID:22047179 in vivo studies reveal a Ni(II)-specific function for the protein.
GO:0050897 cobalt ion binding	IDA PMID:22047179 Metal selectivity of the Escherichia coli nickel metallochap...	KEEP AS NON CORE	Summary: IDA annotation for cobalt ion binding from Kaluarachchi et al. (2011). SlyD binds Co(II) with appreciable affinity but lower than Ni(II) or Zn(II). Reason: Cobalt binding is experimentally demonstrated in vitro but likely not physiologically relevant. In vivo, SlyD functions specifically in nickel homeostasis (PMID:22047179).
GO:0008270 zinc ion binding	IDA PMID:8300624 An Escherichia coli protein consisting of a domain homologou...	KEEP AS NON CORE	Summary: IDA annotation for zinc ion binding from Wuelfing et al. (1994). The original characterization of SlyD showed it binds Ni2+ and Zn2+ tightly with 1:1 stoichiometry. Reason: Zinc binding is experimentally demonstrated but likely not the primary in vivo function. Same reasoning as the other zinc binding annotation. Supporting Evidence: PMID:8300624 The protein binds Ni2+ and Zn2+ tightly with 1:1 stoichiometry, Cu2+ and Co2+ with lower affinity, and Mn2+, Fe2+, Fe3+, Mg2+, and Ca2+ hardly at all.
GO:0016151 nickel cation binding	IDA PMID:19645725 The interaction of the Escherichia coli protein SlyD with ni...	ACCEPT	Summary: IDA annotation for nickel cation binding from Martino et al. (2009). NMR studies showed nickel binding causes conformational rearrangements in the PPIase domain, modulating isomerase activity. Reason: Nickel binding is well-established and directly relevant to regulation of SlyD's PPIase activity and its metallochaperone function. Supporting Evidence: PMID:19645725 the interaction of SlyD with nickel ions entails participation of the novel structural features of the PPIase domain, eliciting structural alterations of the catalytic pocket
GO:0016151 nickel cation binding	IDA PMID:19947632 The Ni(II)-binding properties of the metallochaperone SlyD.	ACCEPT	Summary: IDA annotation for nickel cation binding from Kaluarachchi et al. (2009). ESI-MS showed SlyD binds up to 7 nickel ions in a noncooperative manner with submicromolar affinity. Cysteine residues in the C-terminal domain confer tighter affinity and increased binding capacity. Reason: Detailed characterization of SlyD's nickel binding properties directly related to its metallochaperone function. Supporting Evidence: PMID:19947632 SlyD binds up to seven nickel ions in a noncooperative manner with submicromolar affinity (<2 microM, upper limit)
GO:0016151 nickel cation binding	IDA PMID:8300624 An Escherichia coli protein consisting of a domain homologou...	ACCEPT	Summary: IDA annotation for nickel cation binding from Wuelfing et al. (1994). The original characterization showed tight Ni2+ binding. Reason: The first report of SlyD's nickel binding activity, consistent with subsequent studies showing up to 7 Ni ions bound. Supporting Evidence: PMID:8300624 The protein binds Ni2+ and Zn2+ tightly with 1:1 stoichiometry
GO:0003755 peptidyl-prolyl cis-trans isomerase activity	IMP PMID:17720786 The peptidyl-prolyl isomerase activity of SlyD is not requir...	ACCEPT	Summary: IMP annotation for PPIase activity from Zhang et al. (2007). Mutations that decrease PPIase activity (I42S, F132Y) do not produce corresponding decreases in hydrogenase production, demonstrating that PPIase activity is separable from the metallochaperone function. Reason: This IMP evidence supports the existence of PPIase activity in SlyD, even though the study's main finding is that PPIase is NOT required for hydrogenase maturation. The mutant phenotype evidence confirms PPIase is a real enzymatic activity of SlyD. Supporting Evidence: PMID:17720786 Mutations that result in deficient PPIase activity do not produce corresponding decreases in the other activities of SlyD in vitro or in hydrogenase production levels in vivo.
GO:0050821 protein stabilization	IMP PMID:17971396 Solubilization of aggregation-prone heterologous proteins by...	KEEP AS NON CORE	Summary: IMP annotation for protein stabilization from Han et al. (2007). SlyD was effective as a fusion partner in preventing aggregation and increasing solubility of aggregation-prone heterologous proteins. SlyD sequesters interactive surfaces of heterologous proteins associated with inclusion body formation. Reason: The cited row uses an engineered covalent-fusion system, but independent in-vivo evidence shows that SlyD is required to stabilize the phiX174 E lysis protein. Protein stabilization is therefore a genuine client-specific process, although it is not one of SlyD's broadly acting core functions. Supporting Evidence: PMID:17971396 SlyD was very effective in sequestering interactive surfaces of heterologous proteins associated with non-specific protein-protein interactions and the formation of inclusion bodies PMID:12100551 Our results indicate that SlyD is required for stabilizing the E protein and allowing it to accumulate to the levels required to exert its lytic effect.
GO:0009408 response to heat	IEP PMID:17971396 Solubilization of aggregation-prone heterologous proteins by...	KEEP AS NON CORE	Summary: IEP annotation for response to heat from Han et al. (2007). SlyD synthesis increased 3.37-fold under heat shock conditions compared to non-stress conditions, even when 29 out of 858 soluble proteins were eliminated by the stress. Reason: SlyD upregulation under heat stress is supported by expression profiling, but this is an IEP annotation (expression pattern) rather than functional evidence. The heat stress response may reflect SlyD's general chaperone properties but is not its primary function. Supporting Evidence: PMID:17971396 a 3.37-fold increase induced by heat shock treatment was observed in the synthesis level of SlyD compared with a non-stress condition
GO:0005515 protein binding	IPI PMID:15569666 A role for SlyD in the Escherichia coli hydrogenase biosynth...	KEEP AS NON CORE	Summary: IPI annotation for protein binding from Zhang et al. (2005) showing SlyD-HypB interaction. Sequential peptide affinity purification revealed SlyD in complex with HypB. Deletion of slyD resulted in reduced hydrogenase activity and diminished nickel accumulation. Reason: The interaction is required for hydrogenase maturation, but HypB is the upstream nickel donor to SlyD. This IPI row therefore supports complex formation and nickel acquisition, not SlyD-mediated delivery to a target protein. Supporting Evidence: PMID:15569666 Deletion of the slyD gene resulted in a marked reduction of the hydrogenase activity in cell extracts
GO:0003755 peptidyl-prolyl cis-trans isomerase activity	IDA PMID:9188461 The Escherichia coli SlyD is a metal ion-regulated peptidyl-...	ACCEPT	Summary: IDA annotation for PPIase activity from Hottenrott et al. (1997). Directly measured catalytic activity with kcat/Km of 29,600 M-1 s-1 for Suc-Ala-Phe-Pro-Arg-4-nitroanilide substrate. PPIase activity is of the FKBP type and is reversibly regulated by Ni2+ binding. Reason: Direct enzymatic assay demonstrating PPIase catalytic activity. This is the definitive experimental evidence for SlyD's PPIase function. Supporting Evidence: PMID:9188461 Only when using trypsin instead of chymotrypsin as helper enzyme in the PPIase assay, the enzymatic activity of full-length SlyD and its N-terminal fragment can be measured.
GO:0170061 nickel chaperone activity	IMP PMID:15569666 A role for SlyD in the Escherichia coli hydrogenase biosynth...	NEW	Summary: NEW annotation for nickel chaperone activity. SlyD functions as a nickel metallochaperone that participates in the nickel insertion step of [NiFe]-hydrogenase metallocenter assembly. Deletion of slyD results in reduced hydrogenase activity, which is rescued by excess nickel but not zinc (PMID:15569666). SlyD interacts with HypB and stimulates nickel release from HypB's high-affinity Ni(II)-binding site (PMID:17426034). SlyD also directly interacts with HycE, the hydrogenase 3 large subunit (PMID:21185288). Reason: Nickel metallochaperone activity is one of SlyD's most well-characterized and biologically important functions. GO:0170061 "nickel chaperone activity" (defined as "Directly binding to and delivering nickel ions to a target protein") precisely describes SlyD's role in delivering nickel to [NiFe]-hydrogenase. This function is supported by multiple studies (PMID:15569666, PMID:17426034, PMID:21185288, PMID:22047179) and requires the chaperone domain and C-terminal metal-binding tail but not the PPIase activity (PMID:17720786). IMP is used because the anchor paper establishes the activity through slyD deletion, metal rescue, and hydrogenase phenotypes; the delivery mechanism is a synthesis across complementary biochemical and interaction studies rather than a single direct visualization of nickel transfer. Supporting Evidence: PMID:15569666 These experiments demonstrate that SlyD has a role in the nickel insertion step of the hydrogenase maturation pathway PMID:17426034 SlyD stimulates release of nickel from the high affinity Ni(II)-binding site of HypB, an activity that is also disrupted by mutations that affect complex formation.

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holdase chaperone activity

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