SMX2 (YFL017W-A) encodes Sm protein G (SmG), a 77-residue Sm-fold protein. It is one of the seven essential canonical Sm proteins (SmB, SmD1, SmD2, SmD3, SmE, SmF and SmG) that form the heptameric Sm ring, the core scaffold of the spliceosomal U1, U2, U4 and U5 snRNPs. SmG first associates with SmE and SmF in an F-E-G subcomplex. In the assembled ring it binds a uridine of the snRNA Sm site through a Phe35-Asn37-Arg64 triad, contacts the neighbouring SmE through Arg23, and occurs as a single copy per snRNP core. In S. cerevisiae SmG has been identified by biochemical purification and mass spectrometry in U1, U2 and U5 snRNPs, the U4/U6.U5 tri-snRNP, prespliceosomes, the Cef1/CWC complex and the penta-snRNP, and it is present in cryo-EM structures of yeast spliceosomes. The gene is essential. Single alanine substitutions in its RNA-binding triad are tolerated, but combined triad mutations cause temperature-sensitive growth, and pairing them with RNA-site mutations in other Sm subunits is lethal. This indicates that the Sm ring tolerates the loss of one RNA contact site but not two. SmG acts mainly in the nucleus, in pre-mRNA splicing; snRNP biogenesis may involve a cytoplasmic precursor stage.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000243 commitment complex | NAS PMID:9150140 Cross-intron bridging interactions in the yeast commitment c... | KEEP AS NON CORE | Summary: Commitment complex (CC1/CC2) is the earliest yeast spliceosomal complex and is defined by U1 snRNP bound to the pre-mRNA; SmG enters it as part of the U1 snRNP Sm core. Reason: SmG is a stable U1 snRNP core protein (PMID:9012791), and the commitment complex contains U1 snRNP (PMID:9150140, PMID:2529976). The term is correct by membership but describes one transient stage of a shared structural scaffold; the core localization is the snRNPs themselves. The NAS references do not assay SmG directly. Supporting Evidence: PMID:9150140 It contains U1 snRNP as well as Mud2p, which resembles human U2AF65. PMID:2529976 U1 snRNP and a substrate containing both a 5' splice site and a branchpoint sequence are required for optimal formation of this commitment complex. PMID:9012791 These six proteins were sequenced as described above and identified as the yeast homologs of the human Sm proteins D1, D2, D3, E, F, and G |
| GO:0000245 spliceosomal complex assembly | NAS PMID:11720284 Biochemical and genetic analyses of the U5, U6, and U4/U6 x ... | KEEP AS NON CORE | Summary: Spliceosomal complex assembly. SmG enters each spliceosome as part of the Sm cores of U1, U2 and U4/U6.U5 snRNPs. Reason: Sm-ring proteins are structural components of the snRNPs whose stepwise recruitment builds the spliceosome (PMID:16618970), so SmG contributes structure to the assembling particle. The specific direct evidence in yeast is genetic: SmG RNA-site and interface alleles are synthetically lethal with loss of the U2 snRNP Lea1-Msl1 subassembly (PMID:27417296). This is a sub-process of the core process (mRNA splicing via spliceosome) and is kept as non-core. Supporting Evidence: PMID:27417296 We surmise that the function or structural integrity of the yeast U2 snRNP is especially sensitive to otherwise benign perturbations of the RNA binding or subunit interfaces of the Sm ring when either component of the Lea1•Msl1 subassembly of the U2 snRNP is missing. PMID:27417296 Seven different Sm proteins (B, D1, D2, D3, E, F, and G) assemble into a toroidal ring that forms the core scaffold of the U1, U2, U4, and U5 small ribonuclear proteins (snRNPs) that orchestrate pre-mRNA splicing |
| GO:0000387 spliceosomal snRNP assembly | NAS PMID:11720285 The yeast U5 snRNP coisolated with the U1 snRNP has an unexp... | ACCEPT | Summary: Spliceosomal snRNP assembly. SmG is one of the seven Sm proteins that assemble, via the F-E-G subcomplex, into the heptameric ring around the snRNA Sm site, forming the snRNP core. Reason: The Sm ring is the product of snRNP core assembly, and SmG contributes structure to it directly: it binds SmE (PMID:9528767), is present once per snRNP core (PMID:11302706), and its Sm-site RNA-binding residues are needed in combination with those of other Sm subunits for viability (PMID:27417296). Being a subunit that self-assembles into the complex is participation in its assembly, not mere necessity. Supporting Evidence: PMID:9528767 We observed interactions between SmB and SmD3, SmE and SmF, and SmE and SmG. PMID:11302706 These results indicate that there is only a single copy of each Sm protein in the spliceosomal snRNP core domain and therefore strongly support the heptamer ring model of the spliceosomal snRNP core domain. PMID:27417296 These all-against-all results for SmG suggest that six intact RNA binding sites in the Sm ring can suffice for in vivo function, but five sites may not. |
| GO:0000395 mRNA 5'-splice site recognition | NAS PMID:2529976 Identification of functional U1 snRNA-pre-mRNA complexes com... | KEEP AS NON CORE | Summary: mRNA 5'-splice site recognition, annotated by ComplexPortal from U1 snRNP literature. 5'-splice site recognition is carried out by U1 snRNA base pairing assisted by U1-specific proteins; SmG is part of the U1 Sm core. Reason: SmG is a U1 snRNP core component (PMID:9012791), and the U1 snRNP mediates 5'-splice site recognition in commitment complex formation (PMID:2529976). There is no evidence that SmG itself contacts the 5' splice site; its role is the shared structural Sm core, and genetic data show SmG mutations are relatively insensitive to loss of U1-specific subunits (PMID:27417296). Kept as non-core rather than removed because the Sm core is an integral part of the U1 particle that performs the step. Supporting Evidence: PMID:2529976 U1 snRNP and a substrate containing both a 5' splice site and a branchpoint sequence are required for optimal formation of this commitment complex. PMID:9012791 These six proteins were sequenced as described above and identified as the yeast homologs of the human Sm proteins D1, D2, D3, E, F, and G |
| GO:0000398 mRNA splicing, via spliceosome | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the SmG PAINT node PTN000058285, whose descendants include SMX2 (PTHR10553:SF2), S. pombe smg1, T. brucei Q382A6 and human SNRPG (SF26). SMX2 appears among the donors through its own experimental annotations. Reason: mRNA splicing via the spliceosome is the core process of SmG. SMX2 lies inside the SmG clade (PANTHER subfamily SF2), and yeast evidence places it in all spliceosomal snRNPs with genetic data showing its RNA-binding triad is functionally required in combination with other Sm subunits (PMID:27417296). The IBA reflects an inherited, conserved function. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000058285 SUPPORTS TRANSFER SmG node; SMX2 is in PTHR10553:SF2 beneath it and has its own experimental snRNP evidence. Supporting Evidence: file:yeast/SMX2/SMX2-uniprot.txt PTHR10553:SF2; SMALL NUCLEAR RIBONUCLEOPROTEIN G PMID:27417296 Seven different Sm proteins (B, D1, D2, D3, E, F, and G) assemble into a toroidal ring that forms the core scaffold of the U1, U2, U4, and U5 small ribonuclear proteins (snRNPs) that orchestrate pre-mRNA splicing PMID:27417296 These all-against-all results for SmG suggest that six intact RNA binding sites in the Sm ring can suffice for in vivo function, but five sites may not. |
| GO:0000398 mRNA splicing, via spliceosome | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from IPR034098 (Sm_G) to mRNA splicing via spliceosome. Reason: The Sm_G signature identifies canonical SmG proteins of the Sm ring and the mapping is consistent with the experimental and phylogenetic evidence for SMX2. Supporting Evidence: file:yeast/SMX2/SMX2-uniprot.txt IPR034098; Sm_G. PMID:27417296 Seven different Sm proteins (B, D1, D2, D3, E, F, and G) assemble into a toroidal ring that forms the core scaffold of the U1, U2, U4, and U5 small ribonuclear proteins (snRNPs) that orchestrate pre-mRNA splicing |
| GO:0000398 mRNA splicing, via spliceosome | IPI PMID:10377396 Purification of the yeast U4/U6.U5 small nuclear ribonucleop... | ACCEPT | Summary: IPI from purification of the yeast U4/U6.U5 tri-snRNP, which contains the seven canonical Sm core proteins. Reason: Physical presence in the tri-snRNP, together with presence in U1, U2 and U5 snRNPs and genetic evidence, supports a direct role in splicing. Supporting Evidence: PMID:10377396 In addition to the seven canonical core Sm proteins, there are a set of U6 snRNP specific Sm proteins PMID:27417296 Seven different Sm proteins (B, D1, D2, D3, E, F, and G) assemble into a toroidal ring that forms the core scaffold of the U1, U2, U4, and U5 small ribonuclear proteins (snRNPs) that orchestrate pre-mRNA splicing |
| GO:0000398 mRNA splicing, via spliceosome | NAS PMID:11720284 Biochemical and genetic analyses of the U5, U6, and U4/U6 x ... | ACCEPT | Summary: NAS from purified yeast U5, U6 and tri-snRNPs (PMID:11720284), which contain the canonical Sm core. Reason: Consistent with the core role of SmG as an Sm-ring subunit of the splicing snRNPs. Supporting Evidence: PMID:11720284 The yeast U5 snRNP is composed of the two variants of U5 snRNA, six U5-specific proteins and the 7 proteins of the canonical Sm core. PMID:27417296 Seven different Sm proteins (B, D1, D2, D3, E, F, and G) assemble into a toroidal ring that forms the core scaffold of the U1, U2, U4, and U5 small ribonuclear proteins (snRNPs) that orchestrate pre-mRNA splicing |
| GO:0000398 mRNA splicing, via spliceosome | NAS PMID:16618970 Arrested yeast splicing complexes indicate stepwise snRNP re... | ACCEPT | Summary: NAS from analysis of arrested yeast spliceosomes in which the common Sm proteins were identified with U2 snRNP-containing prespliceosomes. Reason: Consistent with the core role of SmG in pre-mRNA splicing. Supporting Evidence: PMID:16618970 Multiple known U2 snRNP proteins, including SF3a and SF3b components as well as the common set of Sm proteins, were identified in both purifications. PMID:27417296 Seven different Sm proteins (B, D1, D2, D3, E, F, and G) assemble into a toroidal ring that forms the core scaffold of the U1, U2, U4, and U5 small ribonuclear proteins (snRNPs) that orchestrate pre-mRNA splicing |
| GO:0000398 mRNA splicing, via spliceosome | NAS PMID:9150140 Cross-intron bridging interactions in the yeast commitment c... | ACCEPT | Summary: NAS from the commitment complex paper (BBP/Msl5 bridging), which concerns U1 snRNP-containing commitment complexes. Reason: The cited paper does not assay SmG directly, but the claim (participation in mRNA splicing via spliceosome) is well supported for SMX2 by other evidence and is its core process. Supporting Evidence: PMID:9150140 It contains U1 snRNP as well as Mud2p, which resembles human U2AF65. PMID:27417296 Seven different Sm proteins (B, D1, D2, D3, E, F, and G) assemble into a toroidal ring that forms the core scaffold of the U1, U2, U4, and U5 small ribonuclear proteins (snRNPs) that orchestrate pre-mRNA splicing |
| GO:0003674 molecular_function | ND GO_REF:0000015 | MODIFY | Summary: ND annotation to molecular_function root from SGD. Reason: An informative activity can be assigned: SmG is part of the Sm ring that binds the uridine-rich Sm site of U snRNAs. In the human U1 snRNP structure SmG captures a uridine of the Sm site, the equivalent yeast residues (Phe35, Asn37, Arg64) were mutated, and combined mutations give temperature-sensitive or synthetic-lethal phenotypes (PMID:27417296). Because the binding site is formed by the ring, the replacement is contributes_to snRNA binding. Proposed replacements: snRNA binding Supporting Evidence: PMID:27417296 The SmG subunit captures a uridine nucleotide of the U1 RNA Sm site. PMID:27417296 Thus, compound mutations of the SmG RNA binding site elicited a progressive temperature-sensitive (ts) growth defect. PMID:27417296 These all-against-all results for SmG suggest that six intact RNA binding sites in the Sm ring can suffice for in vivo function, but five sites may not. |
| GO:0003723 RNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: IBA contributes_to RNA binding from the deeper PAINT node PTN000058283 (spanning SmG and Lsm7), with yeast LSM7 as the listed donor. Reason: RNA binding is conserved across the SmG/Lsm7 branch (the family review scopes it family-wide) and the contributes_to qualifier correctly reflects that the RNA-binding surface is formed by the heptameric ring. For SMX2 the more specific claim is contributes_to snRNA binding (see the ND molecular_function row), but at the node this broader term is the right granularity. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000058283 SUPPORTS TRANSFER Node above both SmG and Lsm7 subfamilies; RNA binding by ring subunits is conserved across both. Supporting Evidence: PMID:27417296 The SmG subunit captures a uridine nucleotide of the U1 RNA Sm site. PMID:27417296 These all-against-all results for SmG suggest that six intact RNA binding sites in the Sm ring can suffice for in vivo function, but five sites may not. |
| GO:0003723 RNA binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from IPR047575 (Sm domain) to RNA binding. Reason: Correct for SMX2, whose Sm fold contributes a nucleotide-binding triad to the Sm ring (PMID:27417296). The row says enables while the activity is a property of the ring; it is accepted as a true general statement, with the precise claim recorded in core_functions. Supporting Evidence: PMID:27417296 The SmG subunit captures a uridine nucleotide of the U1 RNA Sm site. file:yeast/SMX2/SMX2-uniprot.txt IPR034098; Sm_G. |
| GO:0005515 protein binding | IPI PMID:18719252 High-quality binary protein interaction map of the yeast int... | REMOVE | Summary: Yeast two-hybrid (binary interactome) interaction with SME1 (SmE). Reason: Generic protein binding is uninformative. The SmG-SmE interaction is real and well established (PMID:9528767), but it is a subunit contact within the Sm ring and is captured by the snRNP complex memberships and snRNP assembly terms. No more specific molecular function term is appropriate. Removal does not dispute the interaction. Supporting Evidence: PMID:9528767 We observed interactions between SmB and SmD3, SmE and SmF, and SmE and SmG. |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: Interaction with SME1 (SmE) from a large-scale interactome study. Reason: Generic protein binding is uninformative; the SmG-SmE contact is an intra-ring subunit interaction already represented by complex membership. Removal does not dispute the interaction. Supporting Evidence: PMID:9528767 We observed interactions between SmB and SmD3, SmE and SmF, and SmE and SmG. |
| GO:0005515 protein binding | IPI PMID:9528767 Interactions within the yeast Sm core complex: from proteins... | REMOVE | Summary: Two-hybrid and GST pull-down showing direct SmE-SmG interaction (PMID:9528767). Reason: The direct SmE-SmG interaction is experimentally established and underlies the F-E-G Sm subcomplex, but bare protein binding is uninformative and no more specific molecular function term applies. The biology is captured by spliceosomal snRNP assembly and snRNP complex membership. Removal does not dispute the interaction. Supporting Evidence: PMID:9528767 We observed interactions between SmB and SmD3, SmE and SmF, and SmE and SmG. PMID:27417296 Seven different Sm proteins (B, D1, D2, D3, E, F, and G) assemble into a toroidal ring that forms the core scaffold of the U1, U2, U4, and U5 small ribonuclear proteins (snRNPs) that orchestrate pre-mRNA splicing |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping to nucleus (UniProt location is by similarity to S. pombe smg1). Reason: The spliceosomal snRNPs in which SmG resides function in the nucleus. Supporting Evidence: file:yeast/SMX2/SMX2-uniprot.txt Component of the Sm core complex, present in spliceosomal snRNP U1, U2, U4/U6 and U5. PMID:27417296 Seven different Sm proteins (B, D1, D2, D3, E, F, and G) assemble into a toroidal ring that forms the core scaffold of the U1, U2, U4, and U5 small ribonuclear proteins (snRNPs) that orchestrate pre-mRNA splicing |
| GO:0005634 nucleus | ISS GO_REF:0000024 | ACCEPT | Summary: ISS from S. pombe smg1 (O74966), which shares PANTHER subfamily SF2 with SMX2. Reason: Same subfamily, and the nuclear location follows from SmG membership in spliceosomal snRNPs. Supporting Evidence: file:yeast/SMX2/SMX2-uniprot.txt PTHR10553:SF2; SMALL NUCLEAR RIBONUCLEOPROTEIN G file:yeast/SMX2/SMX2-uniprot.txt Component of the Sm core complex, present in spliceosomal snRNP U1, U2, U4/U6 and U5. |
| GO:0005634 nucleus | NAS PMID:11720284 Biochemical and genetic analyses of the U5, U6, and U4/U6 x ... | ACCEPT | Summary: NAS, nucleus, from purified yeast U5/U6/tri-snRNPs. Reason: Nuclear snRNPs; consistent. Supporting Evidence: PMID:11720284 The yeast U5 snRNP is composed of the two variants of U5 snRNA, six U5-specific proteins and the 7 proteins of the canonical Sm core. |
| GO:0005634 nucleus | NAS PMID:16618970 Arrested yeast splicing complexes indicate stepwise snRNP re... | ACCEPT | Summary: NAS, nucleus, from in vivo arrested spliceosome analysis. Reason: Spliceosome assembly is nuclear; consistent. Supporting Evidence: PMID:16618970 Multiple known U2 snRNP proteins, including SF3a and SF3b components as well as the common set of Sm proteins, were identified in both purifications. |
| GO:0005634 nucleus | NAS PMID:2529976 Identification of functional U1 snRNA-pre-mRNA complexes com... | ACCEPT | Summary: NAS, nucleus, from commitment complex study. Reason: Consistent with U1 snRNP function in nuclear splicing. Supporting Evidence: PMID:2529976 U1 snRNP and a substrate containing both a 5' splice site and a branchpoint sequence are required for optimal formation of this commitment complex. |
| GO:0005634 nucleus | NAS PMID:9150140 Cross-intron bridging interactions in the yeast commitment c... | ACCEPT | Summary: NAS, nucleus, from commitment complex bridging study. Reason: Consistent with U1 snRNP function in nuclear splicing. Supporting Evidence: PMID:9150140 It contains U1 snRNP as well as Mud2p, which resembles human U2AF65. |
| GO:0005681 spliceosomal complex | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from Sm_G to spliceosomal complex. Reason: SmG is present in spliceosomes at several stages (prespliceosome, precatalytic and catalytic spliceosomes, penta-snRNP); the general term is true and still informative for a protein present across stages. Supporting Evidence: file:yeast/SMX2/SMX2-uniprot.txt IPR034098; Sm_G. PMID:11804584 We characterized a 45S yeast penta-snRNP which contains all five spliceosomal snRNAs and over 60 pre-mRNA splicing factors. |
| GO:0005681 spliceosomal complex | NAS PMID:11720284 Biochemical and genetic analyses of the U5, U6, and U4/U6 x ... | ACCEPT | Summary: NAS spliceosomal complex from U5/tri-snRNP purification. Reason: True; SmG is present in multiple spliceosomal complexes. Supporting Evidence: PMID:11720284 The yeast U5 snRNP is composed of the two variants of U5 snRNA, six U5-specific proteins and the 7 proteins of the canonical Sm core. |
| GO:0005681 spliceosomal complex | NAS PMID:16618970 Arrested yeast splicing complexes indicate stepwise snRNP re... | ACCEPT | Summary: NAS spliceosomal complex from arrested spliceosome analysis. Reason: True; Sm proteins identified with prespliceosomes in vivo. Supporting Evidence: PMID:16618970 Multiple known U2 snRNP proteins, including SF3a and SF3b components as well as the common set of Sm proteins, were identified in both purifications. |
| GO:0005681 spliceosomal complex | NAS PMID:2529976 Identification of functional U1 snRNA-pre-mRNA complexes com... | ACCEPT | Summary: NAS spliceosomal complex from commitment complex study. Reason: True; U1 snRNP-containing commitment complexes include the Sm core. Supporting Evidence: PMID:2529976 U1 snRNP and a substrate containing both a 5' splice site and a branchpoint sequence are required for optimal formation of this commitment complex. |
| GO:0005682 U5 snRNP | IBA GO_REF:0000033 | ACCEPT | Summary: IBA, U5 snRNP, from SmG node PTN000058285 with SMX2 and S. pombe smg1 among donors. Reason: SMX2 is in the SmG subfamily and has direct experimental evidence for U5 snRNP membership. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000058285 SUPPORTS TRANSFER SmG node; SMX2 has its own IDA for U5 snRNP. Supporting Evidence: PMID:11720284 The yeast U5 snRNP is composed of the two variants of U5 snRNA, six U5-specific proteins and the 7 proteins of the canonical Sm core. PMID:11720285 In addition to the Sm core proteins, it contains only two of the U5 snRNP specific proteins, Prp8p and Snu114p. |
| GO:0005682 U5 snRNP | IDA PMID:11720284 Biochemical and genetic analyses of the U5, U6, and U4/U6 x ... | ACCEPT | Summary: IDA, U5 snRNP, from affinity purification of yeast U5 snRNP. Reason: U5 snRNP contains the seven canonical Sm core proteins. Supporting Evidence: PMID:11720284 The yeast U5 snRNP is composed of the two variants of U5 snRNA, six U5-specific proteins and the 7 proteins of the canonical Sm core. |
| GO:0005682 U5 snRNP | IDA PMID:11720285 The yeast U5 snRNP coisolated with the U1 snRNP has an unexp... | ACCEPT | Summary: IDA, U5 snRNP, from purification of the 16S Aar2-U5 snRNP. Reason: The Aar2-U5 snRNP contains the Sm core proteins. Supporting Evidence: PMID:11720285 In addition to the Sm core proteins, it contains only two of the U5 snRNP specific proteins, Prp8p and Snu114p. |
| GO:0005682 U5 snRNP | IPI PMID:11720285 The yeast U5 snRNP coisolated with the U1 snRNP has an unexp... | ACCEPT | Summary: IPI, U5 snRNP, from the Aar2-U5 snRNP study. Reason: Consistent with direct biochemical evidence for U5 snRNP membership. Supporting Evidence: PMID:11720285 In addition to the Sm core proteins, it contains only two of the U5 snRNP specific proteins, Prp8p and Snu114p. |
| GO:0005682 U5 snRNP | NAS PMID:10377396 Purification of the yeast U4/U6.U5 small nuclear ribonucleop... | ACCEPT | Summary: NAS, U5 snRNP, from tri-snRNP purification. Reason: Consistent with U5 snRNP membership. Supporting Evidence: PMID:10377396 In addition to the seven canonical core Sm proteins, there are a set of U6 snRNP specific Sm proteins PMID:11720284 The yeast U5 snRNP is composed of the two variants of U5 snRNA, six U5-specific proteins and the 7 proteins of the canonical Sm core. |
| GO:0005682 U5 snRNP | NAS PMID:11720284 Biochemical and genetic analyses of the U5, U6, and U4/U6 x ... | ACCEPT | Summary: NAS, U5 snRNP, from U5 snRNP purification. Reason: Consistent. Supporting Evidence: PMID:11720284 The yeast U5 snRNP is composed of the two variants of U5 snRNA, six U5-specific proteins and the 7 proteins of the canonical Sm core. |
| GO:0005685 U1 snRNP | IBA GO_REF:0000033 | ACCEPT | Summary: IBA, U1 snRNP, from SmG node PTN000058285. Reason: SMX2 is inside the SmG clade and has direct IDA for U1 snRNP. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000058285 SUPPORTS TRANSFER SmG node; SMX2 has its own IDA for U1 snRNP. Supporting Evidence: PMID:9012791 These six proteins were sequenced as described above and identified as the yeast homologs of the human Sm proteins D1, D2, D3, E, F, and G file:yeast/SMX2/SMX2-uniprot.txt PTHR10553:SF2; SMALL NUCLEAR RIBONUCLEOPROTEIN G |
| GO:0005685 U1 snRNP | IDA PMID:9012791 Identification of the proteins of the yeast U1 small nuclear... | ACCEPT | Summary: IDA, U1 snRNP, from mass spectrometry of purified yeast U1 snRNP. Reason: Mass spectrometry identified SmG among the six Sm proteins of the purified yeast U1 snRNP. Supporting Evidence: PMID:9012791 These six proteins were sequenced as described above and identified as the yeast homologs of the human Sm proteins D1, D2, D3, E, F, and G |
| GO:0005685 U1 snRNP | IDA PMID:9630245 A comprehensive biochemical and genetic analysis of the yeas... | ACCEPT | Summary: IDA, U1 snRNP, from comprehensive analysis of yeast U1 snRNP. Reason: Yeast U1 snRNP contains the seven snRNP core proteins. Supporting Evidence: PMID:9630245 Yeast U1 snRNP therefore contains 16 different proteins, including seven snRNP core proteins |
| GO:0005685 U1 snRNP | NAS PMID:16618970 Arrested yeast splicing complexes indicate stepwise snRNP re... | ACCEPT | Summary: NAS, U1 snRNP, from arrested spliceosome analysis. Reason: Consistent with direct evidence. Supporting Evidence: PMID:9012791 These six proteins were sequenced as described above and identified as the yeast homologs of the human Sm proteins D1, D2, D3, E, F, and G |
| GO:0005686 U2 snRNP | IBA GO_REF:0000033 | ACCEPT | Summary: IBA, U2 snRNP, from SmG node PTN000058285. Reason: SMX2 is in the SmG clade; yeast U2 snRNP Sm proteins are identical to those of U1 (PMID:9012791), and SmG alleles are synthetically lethal with loss of the U2 subunits Lea1/Msl1 (PMID:27417296). Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000058285 SUPPORTS TRANSFER SmG node; yeast-specific U2 snRNP Sm composition data support SMX2. Supporting Evidence: PMID:9012791 Sequencing of the proteins from the yeast core U2 snRNP preparation revealed that they were identical to the Sm proteins of the yeast U1 snRNP. PMID:27417296 We surmise that the function or structural integrity of the yeast U2 snRNP is especially sensitive to otherwise benign perturbations of the RNA binding or subunit interfaces of the Sm ring when either component of the Lea1•Msl1 subassembly of the U2 snRNP is missing. |
| GO:0005686 U2 snRNP | NAS PMID:16618970 Arrested yeast splicing complexes indicate stepwise snRNP re... | ACCEPT | Summary: NAS, U2 snRNP, from arrested spliceosome analysis. Reason: The common Sm proteins co-purify with U2 snRNP proteins. Supporting Evidence: PMID:16618970 Multiple known U2 snRNP proteins, including SF3a and SF3b components as well as the common set of Sm proteins, were identified in both purifications. PMID:9012791 Sequencing of the proteins from the yeast core U2 snRNP preparation revealed that they were identical to the Sm proteins of the yeast U1 snRNP. |
| GO:0005687 U4 snRNP | IBA GO_REF:0000033 | ACCEPT | Summary: IBA, U4 snRNP, from SmG node PTN000058285. Reason: SMX2 is in the SmG clade and is present in the U4/U6.U5 tri-snRNP, where U4 snRNA carries the Sm ring. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000058285 SUPPORTS TRANSFER SmG node; SMX2 has its own experimental tri-snRNP evidence. Supporting Evidence: PMID:10377396 In addition to the seven canonical core Sm proteins, there are a set of U6 snRNP specific Sm proteins file:yeast/SMX2/SMX2-uniprot.txt Component of the Sm core complex, present in spliceosomal snRNP U1, U2, U4/U6 and U5. |
| GO:0005687 U4 snRNP | IPI PMID:10377396 Purification of the yeast U4/U6.U5 small nuclear ribonucleop... | ACCEPT | Summary: IPI, U4 snRNP, from tri-snRNP purification. Reason: The tri-snRNP contains the canonical Sm core, which in this particle is carried by U4 and U5 snRNAs. Supporting Evidence: PMID:10377396 In addition to the seven canonical core Sm proteins, there are a set of U6 snRNP specific Sm proteins |
| GO:0005687 U4 snRNP | NAS PMID:11720284 Biochemical and genetic analyses of the U5, U6, and U4/U6 x ... | ACCEPT | Summary: NAS, U4 snRNP, from U5/U6/tri-snRNP study. Reason: Consistent. Supporting Evidence: PMID:11720284 The yeast U5 snRNP is composed of the two variants of U5 snRNA, six U5-specific proteins and the 7 proteins of the canonical Sm core. file:yeast/SMX2/SMX2-uniprot.txt Component of the Sm core complex, present in spliceosomal snRNP U1, U2, U4/U6 and U5. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: UniProt subcellular-location mapping to cytoplasm (UniProt location by similarity to S. pombe smg1). Reason: Sm proteins assemble onto snRNAs in snRNP biogenesis, and yeast has a cytoplasmic precursor U5 snRNP (PMID:17934474). Cytoplasmic presence is plausible but peripheral to the nuclear splicing function. Supporting Evidence: PMID:17934474 We present evidence for a cytoplasmic precursor U5 snRNP in yeast that lacks the mature U5 snRNP component Brr2p and depends on a nuclear localization signal in Prp8p for its efficient nuclear import. |
| GO:0005737 cytoplasm | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS, cytoplasm, from S. pombe smg1 (same PANTHER subfamily SF2). Reason: Plausible for the biogenesis phase of the Sm core; not the core functional location. Supporting Evidence: PMID:17934474 We present evidence for a cytoplasmic precursor U5 snRNP in yeast that lacks the mature U5 snRNP component Brr2p and depends on a nuclear localization signal in Prp8p for its efficient nuclear import. file:yeast/SMX2/SMX2-uniprot.txt PTHR10553:SF2; SMALL NUCLEAR RIBONUCLEOPROTEIN G |
| GO:0005737 cytoplasm | NAS PMID:17934474 prp8 mutations that cause human retinitis pigmentosa lead to... | KEEP AS NON CORE | Summary: NAS, cytoplasm, from the study of a cytoplasmic precursor U5 snRNP in yeast. Reason: The paper describes a cytoplasmic precursor U5 snRNP; the Sm core is part of U5 snRNP, so SmG is plausibly present in it. Peripheral to the core nuclear function. Supporting Evidence: PMID:17934474 We present evidence for a cytoplasmic precursor U5 snRNP in yeast that lacks the mature U5 snRNP component Brr2p and depends on a nuclear localization signal in Prp8p for its efficient nuclear import. |
| GO:0008150 biological_process | ND GO_REF:0000015 | MODIFY | Summary: ND annotation to biological_process root from SGD. Reason: A biological process is well established: SmG participates in nuclear pre-mRNA splicing as a structural Sm-ring subunit of the spliceosomal snRNPs. Proposed replacements: mRNA splicing, via spliceosome Supporting Evidence: PMID:27417296 Seven different Sm proteins (B, D1, D2, D3, E, F, and G) assemble into a toroidal ring that forms the core scaffold of the U1, U2, U4, and U5 small ribonuclear proteins (snRNPs) that orchestrate pre-mRNA splicing PMID:27417296 These all-against-all results for SmG suggest that six intact RNA binding sites in the Sm ring can suffice for in vivo function, but five sites may not. |
| GO:0032991 protein-containing complex | IEA GO_REF:0000117 | TOO GENERAL | Summary: ARBA machine-learning annotation to protein-containing complex. Reason: True but uninformative; the specific snRNP and spliceosome complexes accepted elsewhere in this review entail it. Supporting Evidence: file:yeast/SMX2/SMX2-uniprot.txt Component of the Sm core complex, present in spliceosomal snRNP U1, U2, U4/U6 and U5. |
| GO:0034719 SMN-Sm protein complex | IBA GO_REF:0000033 | REMOVE | Summary: IBA to SMN-Sm protein complex from SmG node PTN000058285, with human SNRPG as the only listed donor. Reason: GO:0034719 is defined as Sm proteins associated with the SMN complex (SMN plus Gemins). The function is real in animals and plausibly in S. pombe (which has an SMN ortholog), but Saccharomyces cerevisiae lacks an SMN ortholog; its Sm assembly machinery is poorly defined, with only a putative Gemin2 homolog, Brr1 (PMID:27417296). The complex cannot form in budding yeast, so the propagation to SMX2 fails because of partner loss in this lineage rather than divergence of SmG itself. Propagation Review Root cause: PROPAGATION BAD Failure modes: LINEAGE OR TAXON MISMATCH COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000058285 SUPPORTS SOURCE BUT NOT TARGET SmG node; supported by human SNRPG, but the SMN partner is absent from S. cerevisiae (UniProt search of taxon 559292 finds no SMN ortholog; SMN1/YHR202W is an unrelated nucleotidase). Supporting Evidence: PMID:27417296 Less is known about the Sm assembly pathway in the simpler model organism Saccharomyces cerevisiae, beyond the fact that budding yeast has, in Brr1, a putative homolog of the key metazoan Sm assembly factor Gemin2 |
| GO:0036261 7-methylguanosine cap hypermethylation | IMP PMID:9528767 Interactions within the yeast Sm core complex: from proteins... | MARK AS OVER ANNOTATED | Summary: IMP, 7-methylguanosine cap hypermethylation, by ComplexPortal from PMID:9528767. In that paper the experiment depleted SmE (and cited earlier SmD1/SmD3 work), not SmG. Reason: Cap trimethylation is catalysed by the methyltransferase Tgs1. The Sm core is required as the RNP context on which this occurs, so depletion of Sm subunits reduces hypermethylation (PMID:9528767). That is necessity, and SmG itself was not tested. Notably, SmG RNA-site and interface alleles showed no synergy with tgs1 deletion (PMID:27417296). The annotation is a complex-level inference applied to every Sm subunit; it is not a function of SMX2. Supporting Evidence: PMID:9528767 depletion of SmE protein affects the snRNA hypermethylation process |
| GO:0046540 U4/U6 x U5 tri-snRNP complex | IDA PMID:10377396 Purification of the yeast U4/U6.U5 small nuclear ribonucleop... | ACCEPT | Summary: IDA, U4/U6 x U5 tri-snRNP complex, from purification of the yeast tri-snRNP. Reason: Canonical Sm core proteins are stable tri-snRNP components. Supporting Evidence: PMID:10377396 In addition to the seven canonical core Sm proteins, there are a set of U6 snRNP specific Sm proteins |
| GO:0046540 U4/U6 x U5 tri-snRNP complex | IDA PMID:10449419 Identification by mass spectrometry and functional analysis ... | ACCEPT | Summary: IDA, U4/U6 x U5 tri-snRNP complex, from mass spectrometry of the yeast tri-snRNP. Reason: Mass spectrometry of the purified tri-snRNP identified the known tri-snRNP proteins, including the Sm core. Supporting Evidence: PMID:10449419 In addition to the known tri-snRNP proteins (only one, Lsm3p, eluded detection), we identified eight previously uncharacterized proteins. file:yeast/SMX2/SMX2-uniprot.txt Component of the Sm core complex, present in spliceosomal snRNP U1, U2, U4/U6 and U5. |
| GO:0046540 U4/U6 x U5 tri-snRNP complex | NAS PMID:11720284 Biochemical and genetic analyses of the U5, U6, and U4/U6 x ... | ACCEPT | Summary: NAS, U4/U6 x U5 tri-snRNP complex. Reason: Consistent with direct evidence. Supporting Evidence: PMID:10377396 In addition to the seven canonical core Sm proteins, there are a set of U6 snRNP specific Sm proteins |
| GO:0071001 U4/U6 snRNP | NAS PMID:11720284 Biochemical and genetic analyses of the U5, U6, and U4/U6 x ... | ACCEPT | Summary: NAS, U4/U6 snRNP. U4 snRNA in the U4/U6 di-snRNP carries the Sm ring. Reason: SmG is part of the U4 Sm core and therefore of U4/U6 particles. Supporting Evidence: file:yeast/SMX2/SMX2-uniprot.txt Component of the Sm core complex, present in spliceosomal snRNP U1, U2, U4/U6 and U5. |
| GO:0071004 U2-type prespliceosome | IBA GO_REF:0000033 | ACCEPT | Summary: IBA, U2-type prespliceosome, from node PTN000058284 with SMX2 as donor. Reason: SMX2 has direct experimental support for presence in prespliceosomes via U1 and U2 snRNPs. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000058284 SUPPORTS TRANSFER SMX2 own IDA is among the descendant evidence for this node. Supporting Evidence: PMID:16618970 Multiple known U2 snRNP proteins, including SF3a and SF3b components as well as the common set of Sm proteins, were identified in both purifications. PMID:16618970 indicating that U1–U2–containing prespliceosomes form in vivo without U5 snRNP |
| GO:0071004 U2-type prespliceosome | IDA PMID:16618970 Arrested yeast splicing complexes indicate stepwise snRNP re... | ACCEPT | Summary: IDA, U2-type prespliceosome, from TAP purification of arrested U1-U2 prespliceosomes in vivo. Reason: The common Sm proteins were identified in the U2 snRNP-containing purifications. Supporting Evidence: PMID:16618970 Multiple known U2 snRNP proteins, including SF3a and SF3b components as well as the common set of Sm proteins, were identified in both purifications. PMID:16618970 indicating that U1–U2–containing prespliceosomes form in vivo without U5 snRNP |
| GO:0071011 precatalytic spliceosome | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA, precatalytic spliceosome, with human SNRPG as donor. Reason: The Sm cores of U2, U5 and U4 snRNPs are present in the precatalytic (B) spliceosome; yeast B-complex cryo-EM structures contain SmG. Correct, but it is a stage-specific context of the shared snRNP scaffold. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN000058285 SUPPORTS TRANSFER SmG node; Sm cores persist into the B complex in yeast. Supporting Evidence: PMID:27417296 Seven different Sm proteins (B, D1, D2, D3, E, F, and G) assemble into a toroidal ring that forms the core scaffold of the U1, U2, U4, and U5 small ribonuclear proteins (snRNPs) that orchestrate pre-mRNA splicing PMID:11804584 We characterized a 45S yeast penta-snRNP which contains all five spliceosomal snRNAs and over 60 pre-mRNA splicing factors. |
| GO:0071013 catalytic step 2 spliceosome | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA, catalytic step 2 spliceosome, with human SNRPG as donor. Reason: U2 and U5 Sm cores remain in catalytic spliceosomes; yeast Cef1/CWC complexes, which resemble late-stage spliceosomes, contain the core Sm proteins (PMID:11884590). Correct but stage-specific. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN000058284 SUPPORTS TRANSFER U2 and U5 Sm cores remain through catalysis. Supporting Evidence: PMID:11884590 including known core Sm proteins and U2 and U5 snRNP components |
| GO:0097526 spliceosomal tri-snRNP complex | IBA GO_REF:0000033 | MODIFY | Summary: IBA, spliceosomal tri-snRNP complex, from SmG node PTN000058285. Reason: Correct but more general than the evidence for budding yeast, which has only the U2-type spliceosome. SMX2 already carries the specific child term U4/U6 x U5 tri-snRNP complex by IDA (PMID:10377396, PMID:10449419). Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000058285 SUPPORTS TRANSFER General term is appropriate at the node; for S. cerevisiae the U2-type child applies. Proposed replacements: U4/U6 x U5 tri-snRNP complex Supporting Evidence: PMID:10377396 In addition to the seven canonical core Sm proteins, there are a set of U6 snRNP specific Sm proteins PMID:10449419 In addition to the known tri-snRNP proteins (only one, Lsm3p, eluded detection), we identified eight previously uncharacterized proteins. |
| GO:1903241 U2-type prespliceosome assembly | NAS PMID:16618970 Arrested yeast splicing complexes indicate stepwise snRNP re... | KEEP AS NON CORE | Summary: NAS, U2-type prespliceosome assembly, from in vivo stepwise snRNP recruitment study. Reason: SmG enters the prespliceosome as part of U1 and U2 snRNPs. Its alleles are especially sensitive to loss of U2 snRNP Lea1/Msl1 (PMID:27417296), consistent with a structural contribution to U2 snRNP function during prespliceosome formation. This is a sub-process of the core splicing role. Supporting Evidence: PMID:16618970 indicating that U1–U2–containing prespliceosomes form in vivo without U5 snRNP PMID:27417296 We surmise that the function or structural integrity of the yeast U2 snRNP is especially sensitive to otherwise benign perturbations of the RNA binding or subunit interfaces of the Sm ring when either component of the Lea1•Msl1 subassembly of the U2 snRNP is missing. |
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Download this section (compressed HTML)Q: Should Sm-ring subunits whose individual nucleotide contacts are structurally defined carry contributes_to snRNA binding (GO:0017069) rather than only the broad RNA binding inherited from the SmG/Lsm7 PAINT node?
Q: How is the Sm ring assembled in S. cerevisiae, which lacks SMN; does Brr1 act as a Gemin2-like chaperone for the F-E-G subcomplex containing SmG?
Experiment: Biochemically test the requirement of the SmG Phe35-Asn37-Arg64 triad for Sm-ring assembly on U snRNA in yeast extracts (e.g. snRNP assembly/stability and U snRNA levels in the F35A-N37A-R64A strain at restrictive temperature), to separate RNA-binding from ring-stability effects.
Core Sm protein Sm G; part of heteroheptameric complex (with Smb1p, Smd1p, Smd2p, Smd3p, Sme1p, and Smx3p) that is part of the spliceosomal U1, U2, U4, and U5 snRNPs; homolog of human Sm G
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