SHM1 encodes the mitochondrial serine hydroxymethyltransferase, a pyridoxal 5'-phosphate-dependent enzyme with an N-terminal mitochondrial transit peptide that reversibly converts L-serine and tetrahydrofolate to glycine and 5,10-methylenetetrahydrofolate. Although it accounts for only about 5% of total cellular SHMT activity, its specific activity in mitochondria is high, and it is a major supplier of one-carbon units for purine, thymidylate and methionine synthesis. Its direction depends on nutrition: on glycine it is the predominant isozyme forming serine from glycine and one-carbon units, and it contributes one-carbon units but little glycine when both amino acids are present. Shm1 acts in parallel with the cytosolic paralog Shm2 and with Gly1 and Agx1 in glycine/serine interconversion; the classical tmp3 mutant is shm1.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004372 glycine hydroxymethyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PANTHER PTN000188065 (SHMT family; E. coli GlyA, human SHMT1/SHMT2, plant and Plasmodium SHMTs); both yeast paralogs are among the experimental sources. Reason: Ser/gly hydroxymethyltransferase activity is ancestral to the whole SHMT family and conserved in SHM1; inheritance is sound. Supporting Evidence: file:yeast/SHM1/SHM1-uniprot.txt FUNCTION: Interconversion of serine and glycine. |
| GO:0004372 glycine hydroxymethyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: IEA from InterPro IPR001085 (serine hydroxymethyltransferase) + RHEA:15481. Reason: Correct core activity (EC 2.1.2.1). Supporting Evidence: file:yeast/SHM1/SHM1-uniprot.txt FUNCTION: Interconversion of serine and glycine. |
| GO:0004372 glycine hydroxymethyltransferase activity | IMP PMID:1100397 Isolation and properties of a thymidylate-less mutant in Sac... | ACCEPT | Summary: IMP from Luzzati 1975: the tmp3 mutant (later shown to be shm1) has a 60% decrease in SHMT specific activity in crude extracts. Reason: Genetic evidence that SHM1 encodes an SHMT activity; consistent with the later cloning that assigned SHM1 to the mitochondrial isozyme. Supporting Evidence: PMID:1100397 Crude extracts of this mutant present a 60% decrease of serine transhydroxymethylase specific activity as compared to a wild-type strain PMID:8132653 subcellular fractionation studies all suggested that the SHM1 gene encodes the mitochondrial SHMT, while the SHM2 gene encodes the cytosolic enzyme |
| GO:0004372 glycine hydroxymethyltransferase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA from ALL-CHORISMATE-PWY-1 (superpathway of chorismate metabolism), assigning the serine hydroxymethyltransferase reaction to SHM1. Reason: The molecular function is correct irrespective of which YeastPathways pathway generated the row. Note that superpathway of chorismate metabolism is a superpathway context in which SHMT only supplies 5,10-methylene-THF; the MF itself is still right. Supporting Evidence: file:yeast/SHM1/SHM1-uniprot.txt FUNCTION: Interconversion of serine and glycine. |
| GO:0004372 glycine hydroxymethyltransferase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA from FOLSYN-PWY-1 (superpathway of tetrahydrofolate biosynthesis and salvage), assigning the serine hydroxymethyltransferase reaction to SHM1. Reason: The molecular function is correct irrespective of which YeastPathways pathway generated the row. Supporting Evidence: file:yeast/SHM1/SHM1-uniprot.txt FUNCTION: Interconversion of serine and glycine. |
| GO:0004372 glycine hydroxymethyltransferase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA from GLYSYN-PWY (glycine biosynthesis I), assigning the serine hydroxymethyltransferase reaction to SHM1. Reason: The molecular function is correct irrespective of which YeastPathways pathway generated the row. Supporting Evidence: file:yeast/SHM1/SHM1-uniprot.txt FUNCTION: Interconversion of serine and glycine. |
| GO:0004372 glycine hydroxymethyltransferase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA from PWY-2201 (folate transformations I), assigning the serine hydroxymethyltransferase reaction to SHM1. Reason: The molecular function is correct irrespective of which YeastPathways pathway generated the row. Supporting Evidence: file:yeast/SHM1/SHM1-uniprot.txt FUNCTION: Interconversion of serine and glycine. |
| GO:0004372 glycine hydroxymethyltransferase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA from PWY3O-20 (folate polyglutamylation), assigning the serine hydroxymethyltransferase reaction to SHM1. Reason: The molecular function is correct irrespective of which YeastPathways pathway generated the row. Note that folate polyglutamylation is a superpathway context in which SHMT only supplies 5,10-methylene-THF; the MF itself is still right. Supporting Evidence: file:yeast/SHM1/SHM1-uniprot.txt FUNCTION: Interconversion of serine and glycine. |
| GO:0004372 glycine hydroxymethyltransferase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA from PWY3O-230 (serine biosynthesis from glyoxylate), assigning the serine hydroxymethyltransferase reaction to SHM1. Reason: The molecular function is correct irrespective of which YeastPathways pathway generated the row. Supporting Evidence: file:yeast/SHM1/SHM1-uniprot.txt FUNCTION: Interconversion of serine and glycine. |
| GO:0004372 glycine hydroxymethyltransferase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA from PWY3O-261 (superpathway of serine and glycine biosynthesis), assigning the serine hydroxymethyltransferase reaction to SHM1. Reason: The molecular function is correct irrespective of which YeastPathways pathway generated the row. Supporting Evidence: file:yeast/SHM1/SHM1-uniprot.txt FUNCTION: Interconversion of serine and glycine. |
| GO:0004372 glycine hydroxymethyltransferase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA from PWY3O-697 (folate interconversions), assigning the serine hydroxymethyltransferase reaction to SHM1. Reason: The molecular function is correct irrespective of which YeastPathways pathway generated the row. Supporting Evidence: file:yeast/SHM1/SHM1-uniprot.txt FUNCTION: Interconversion of serine and glycine. |
| GO:0005739 mitochondrion | HDA PMID:14576278 The proteome of Saccharomyces cerevisiae mitochondria. | ACCEPT | Summary: HDA from a mitochondrial proteome (PMID:14576278) detecting Shm1 in purified mitochondria. Reason: Consistent with the N-terminal transit peptide and fractionation data; Shm1 is the mitochondrial isozyme. Supporting Evidence: PMID:14576278 The proteins of highly pure yeast mitochondria were separated by several independent methods and analyzed by tandem MS PMID:8132653 subcellular fractionation studies all suggested that the SHM1 gene encodes the mitochondrial SHMT, while the SHM2 gene encodes the cytosolic enzyme |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | ACCEPT | Summary: HDA from a mitochondrial proteome (PMID:16823961) detecting Shm1 in purified mitochondria. Reason: Consistent with the N-terminal transit peptide and fractionation data; Shm1 is the mitochondrial isozyme. Supporting Evidence: PMID:16823961 A total of 851 different proteins (PROMITO dataset) were identified PMID:8132653 subcellular fractionation studies all suggested that the SHM1 gene encodes the mitochondrial SHMT, while the SHM2 gene encodes the cytosolic enzyme |
| GO:0005739 mitochondrion | HDA PMID:24769239 Quantitative variations of the mitochondrial proteome and ph... | ACCEPT | Summary: HDA from a mitochondrial proteome (PMID:24769239) detecting Shm1 in purified mitochondria. Reason: Consistent with the N-terminal transit peptide and fractionation data; Shm1 is the mitochondrial isozyme. Supporting Evidence: PMID:24769239 we performed an overall quantitative proteomic and phosphoproteomic study of isolated mitochondria extracted from yeast PMID:8132653 subcellular fractionation studies all suggested that the SHM1 gene encodes the mitochondrial SHMT, while the SHM2 gene encodes the cytosolic enzyme |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN000188068 (mitochondrial SHMT2-like node; human SHMT2, mouse Shmt2, Arabidopsis SHM, SHM1 itself). Reason: Correct; Shm1 belongs to the mitochondrial SHMT lineage and has a cleavable transit peptide. Supporting Evidence: PMID:8132653 subcellular fractionation studies all suggested that the SHM1 gene encodes the mitochondrial SHMT, while the SHM2 gene encodes the cytosolic enzyme |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: IEA from UniProt subcellular location keyword mapping (SL-0173 mitochondrion). Reason: Correct. Supporting Evidence: file:yeast/SHM1/SHM1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion. |
| GO:0005739 mitochondrion | IMP PMID:6271 Two forms of serine transhydroxymethylase, one absent in a t... | ACCEPT | Summary: IMP from Zelikson & Luzzati 1976: of two SHMT forms, one is absent in the tmp3 (shm1) mutant; the missing form is the mitochondrial enzyme. Reason: Deferred to curator (abstract-only, no abstract text); consistent with the later molecular assignment of SHM1 to mitochondria. Supporting Evidence: PMID:6271 Two forms of serine transhydroxymethylase, one absent in a thymidylate-less mutant in Saccharomyces cerevisiae PMID:8132653 subcellular fractionation studies all suggested that the SHM1 gene encodes the mitochondrial SHMT, while the SHM2 gene encodes the cytosolic enzyme |
| GO:0005739 mitochondrion | IMP PMID:9398220 Role of mitochondrial and cytoplasmic serine hydroxymethyltr... | ACCEPT | Summary: IMP from Kastanos et al. 1997: subcellular fractionation of shm mutants shows mitochondrial SHMT activity (5% of total, high specific activity) depends on SHM1. Reason: Experimental localization of the Shm1 activity. Supporting Evidence: PMID:9398220 Cell subfractionation experiments indicated that while only 5% of total activity was localized in the mitochondria, the specific activity in that compartment was much higher than in the cytoplasm PMID:9398220 In Saccharomyces cerevisiae, mitochondrial and cytoplasmic SHMT isozymes are encoded by distinct nuclear genes (SHM1 and SHM2) |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA placing the ALL-CHORISMATE-PWY-1 (superpathway of chorismate metabolism) SHMT reaction in the cytosol, attributed to both paralogs. Reason: Shm1 is the mitochondrial isozyme (transit peptide, fractionation, mitochondrial proteomes); the cytosolic SHMT reaction is catalysed by Shm2. The RCA conversion assigned the pathway compartment to every enzyme of the reaction. Supporting Evidence: PMID:8132653 subcellular fractionation studies all suggested that the SHM1 gene encodes the mitochondrial SHMT, while the SHM2 gene encodes the cytosolic enzyme PMID:9398220 In Saccharomyces cerevisiae, mitochondrial and cytoplasmic SHMT isozymes are encoded by distinct nuclear genes (SHM1 and SHM2) |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA placing the FOLSYN-PWY-1 (superpathway of tetrahydrofolate biosynthesis and salvage) SHMT reaction in the cytosol, attributed to both paralogs. Reason: Shm1 is the mitochondrial isozyme (transit peptide, fractionation, mitochondrial proteomes); the cytosolic SHMT reaction is catalysed by Shm2. The RCA conversion assigned the pathway compartment to every enzyme of the reaction. Supporting Evidence: PMID:8132653 subcellular fractionation studies all suggested that the SHM1 gene encodes the mitochondrial SHMT, while the SHM2 gene encodes the cytosolic enzyme PMID:9398220 In Saccharomyces cerevisiae, mitochondrial and cytoplasmic SHMT isozymes are encoded by distinct nuclear genes (SHM1 and SHM2) |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA placing the GLYSYN-PWY (glycine biosynthesis I) SHMT reaction in the cytosol, attributed to both paralogs. Reason: Shm1 is the mitochondrial isozyme (transit peptide, fractionation, mitochondrial proteomes); the cytosolic SHMT reaction is catalysed by Shm2. The RCA conversion assigned the pathway compartment to every enzyme of the reaction. Supporting Evidence: PMID:8132653 subcellular fractionation studies all suggested that the SHM1 gene encodes the mitochondrial SHMT, while the SHM2 gene encodes the cytosolic enzyme PMID:9398220 In Saccharomyces cerevisiae, mitochondrial and cytoplasmic SHMT isozymes are encoded by distinct nuclear genes (SHM1 and SHM2) |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA placing the PWY-2201 (folate transformations I) SHMT reaction in the cytosol, attributed to both paralogs. Reason: Shm1 is the mitochondrial isozyme (transit peptide, fractionation, mitochondrial proteomes); the cytosolic SHMT reaction is catalysed by Shm2. The RCA conversion assigned the pathway compartment to every enzyme of the reaction. Supporting Evidence: PMID:8132653 subcellular fractionation studies all suggested that the SHM1 gene encodes the mitochondrial SHMT, while the SHM2 gene encodes the cytosolic enzyme PMID:9398220 In Saccharomyces cerevisiae, mitochondrial and cytoplasmic SHMT isozymes are encoded by distinct nuclear genes (SHM1 and SHM2) |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA placing the PWY3O-20 (folate polyglutamylation) SHMT reaction in the cytosol, attributed to both paralogs. Reason: Shm1 is the mitochondrial isozyme (transit peptide, fractionation, mitochondrial proteomes); the cytosolic SHMT reaction is catalysed by Shm2. The RCA conversion assigned the pathway compartment to every enzyme of the reaction. Supporting Evidence: PMID:8132653 subcellular fractionation studies all suggested that the SHM1 gene encodes the mitochondrial SHMT, while the SHM2 gene encodes the cytosolic enzyme PMID:9398220 In Saccharomyces cerevisiae, mitochondrial and cytoplasmic SHMT isozymes are encoded by distinct nuclear genes (SHM1 and SHM2) |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA placing the PWY3O-230 (serine biosynthesis from glyoxylate) SHMT reaction in the cytosol, attributed to both paralogs. Reason: Shm1 is the mitochondrial isozyme (transit peptide, fractionation, mitochondrial proteomes); the cytosolic SHMT reaction is catalysed by Shm2. The RCA conversion assigned the pathway compartment to every enzyme of the reaction. Supporting Evidence: PMID:8132653 subcellular fractionation studies all suggested that the SHM1 gene encodes the mitochondrial SHMT, while the SHM2 gene encodes the cytosolic enzyme PMID:9398220 In Saccharomyces cerevisiae, mitochondrial and cytoplasmic SHMT isozymes are encoded by distinct nuclear genes (SHM1 and SHM2) |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA placing the PWY3O-261 (superpathway of serine and glycine biosynthesis) SHMT reaction in the cytosol, attributed to both paralogs. Reason: Shm1 is the mitochondrial isozyme (transit peptide, fractionation, mitochondrial proteomes); the cytosolic SHMT reaction is catalysed by Shm2. The RCA conversion assigned the pathway compartment to every enzyme of the reaction. Supporting Evidence: PMID:8132653 subcellular fractionation studies all suggested that the SHM1 gene encodes the mitochondrial SHMT, while the SHM2 gene encodes the cytosolic enzyme PMID:9398220 In Saccharomyces cerevisiae, mitochondrial and cytoplasmic SHMT isozymes are encoded by distinct nuclear genes (SHM1 and SHM2) |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA placing the PWY3O-697 (folate interconversions) SHMT reaction in the cytosol, attributed to both paralogs. Reason: Shm1 is the mitochondrial isozyme (transit peptide, fractionation, mitochondrial proteomes); the cytosolic SHMT reaction is catalysed by Shm2. The RCA conversion assigned the pathway compartment to every enzyme of the reaction. Supporting Evidence: PMID:8132653 subcellular fractionation studies all suggested that the SHM1 gene encodes the mitochondrial SHMT, while the SHM2 gene encodes the cytosolic enzyme PMID:9398220 In Saccharomyces cerevisiae, mitochondrial and cytoplasmic SHMT isozymes are encoded by distinct nuclear genes (SHM1 and SHM2) |
| GO:0006545 glycine biosynthetic process | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA glycine biosynthetic process for Shm1 (PTN000188065 IBA). Reason: Shm1 can form glycine (it contributes to prototrophy in gly1 shm2 backgrounds), but 13C-NMR shows the mitochondrial isozyme supplies one-carbon units rather than glycine when both amino acids are present, and Gly1/Shm2 are the main glycine sources. Non-core for Shm1. Supporting Evidence: PMID:9398220 when both serine and glycine were present, the mitochondrial SHMT made a significant contribution of one-carbon units, but not glycine, for purine synthesis PMID:8132653 Gene disruption studies demonstrated that inactivation of SHM1, SHM2, and GLY1 is required to yield yeast that are completely auxotrophic for glycine |
| GO:0006545 glycine biosynthetic process | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: IEA glycine biosynthetic process for Shm1 (InterPro IPR001085 mapping). Reason: Shm1 can form glycine (it contributes to prototrophy in gly1 shm2 backgrounds), but 13C-NMR shows the mitochondrial isozyme supplies one-carbon units rather than glycine when both amino acids are present, and Gly1/Shm2 are the main glycine sources. Non-core for Shm1. Supporting Evidence: PMID:9398220 when both serine and glycine were present, the mitochondrial SHMT made a significant contribution of one-carbon units, but not glycine, for purine synthesis PMID:8132653 Gene disruption studies demonstrated that inactivation of SHM1, SHM2, and GLY1 is required to yield yeast that are completely auxotrophic for glycine |
| GO:0006545 glycine biosynthetic process | RCA GO_REF:0000123 | KEEP AS NON CORE | Summary: RCA glycine biosynthetic process for Shm1 (YeastPathways GLYSYN-PWY RCA). Reason: Shm1 can form glycine (it contributes to prototrophy in gly1 shm2 backgrounds), but 13C-NMR shows the mitochondrial isozyme supplies one-carbon units rather than glycine when both amino acids are present, and Gly1/Shm2 are the main glycine sources. Non-core for Shm1. Supporting Evidence: PMID:9398220 when both serine and glycine were present, the mitochondrial SHMT made a significant contribution of one-carbon units, but not glycine, for purine synthesis PMID:8132653 Gene disruption studies demonstrated that inactivation of SHM1, SHM2, and GLY1 is required to yield yeast that are completely auxotrophic for glycine |
| GO:0006564 L-serine biosynthetic process | RCA GO_REF:0000123 | KEEP AS NON CORE | Summary: YeastPathways RCA from PWY3O-230 (serine biosynthesis from glyoxylate), in which glycine from the glyoxylate route is converted to serine by SHMT. Reason: Supported: on glycine the mitochondrial SHMT is the predominant isozyme making serine from glycine. This is a conditional (gluconeogenic) route, so it is kept as non-core. Supporting Evidence: PMID:9398220 When grown on glycine, the mitochondrial SHMT was the predominant isozyme catalyzing the synthesis of serine from glycine and one-carbon units |
| GO:0006730 one-carbon metabolic process | IGI PMID:9398220 Role of mitochondrial and cytoplasmic serine hydroxymethyltr... | ACCEPT | Summary: IGI with SHM2 from Kastanos et al. 1997: shm1/shm2 single and double mutants define the isozyme contributions to one-carbon units for purine synthesis. Reason: Shm1 provides one-carbon units (5,10-CH2-THF) in mitochondria; this is core. Supporting Evidence: PMID:9398220 when both serine and glycine were present, the mitochondrial SHMT made a significant contribution of one-carbon units, but not glycine, for purine synthesis |
| GO:0006730 one-carbon metabolic process | IMP PMID:1100397 Isolation and properties of a thymidylate-less mutant in Sac... | ACCEPT | Summary: IMP from Luzzati 1975: tmp3 (shm1) mutant requires thymidylate, methionine, adenine and histidine. Reason: These are all one-carbon-dependent end products; consistent with Shm1 supplying one-carbon units. Supporting Evidence: PMID:1100397 a single mendelian gene controls the multiple requirements for thymidylate, methionine, adenine and histidine |
| GO:0009070 serine family amino acid biosynthetic process | RCA GO_REF:0000123 | TOO GENERAL | Summary: YeastPathways RCA from superpathway PWY3O-261. Reason: Correct in a general sense (serine/glycine interconversion) but less informative than the specific processes. Supporting Evidence: PMID:9398220 In Saccharomyces cerevisiae, mitochondrial and cytoplasmic SHMT isozymes are encoded by distinct nuclear genes (SHM1 and SHM2) |
| GO:0030170 pyridoxal phosphate binding | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA pyridoxal phosphate binding (PTN000188065). Reason: Correct cofactor binding; integral to the SHMT activity rather than a separate function. Supporting Evidence: file:yeast/SHM1/SHM1-uniprot.txt Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326; |
| GO:0030170 pyridoxal phosphate binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: IEA pyridoxal phosphate binding (InterPro IPR001085/IPR019798 PLP attachment site). Reason: Correct cofactor binding; integral to the SHMT activity rather than a separate function. Supporting Evidence: file:yeast/SHM1/SHM1-uniprot.txt Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326; |
| GO:0035999 folate cycle | IEA GO_REF:0000120 | ACCEPT | Summary: IEA from InterPro IPR001085 + UniPathway UPA00193 (tetrahydrofolate interconversion). Reason: Correct core process: SHMT converts THF to 5,10-methylene-THF. Supporting Evidence: PMID:9398220 when both serine and glycine were present, the mitochondrial SHMT made a significant contribution of one-carbon units, but not glycine, for purine synthesis |
| GO:0035999 folate cycle | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA from FOLSYN-PWY-1 (superpathway of tetrahydrofolate biosynthesis and salvage). Reason: Correct; SHMT is a central THF-interconverting enzyme. Supporting Evidence: PMID:9398220 when both serine and glycine were present, the mitochondrial SHMT made a significant contribution of one-carbon units, but not glycine, for purine synthesis |
| GO:0035999 folate cycle | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA from PWY-2201 (folate transformations I). Reason: Correct; SHMT is a central THF-interconverting enzyme. Supporting Evidence: PMID:9398220 when both serine and glycine were present, the mitochondrial SHMT made a significant contribution of one-carbon units, but not glycine, for purine synthesis |
| GO:0046417 chorismate metabolic process | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA from ALL-CHORISMATE-PWY-1 (superpathway of chorismate metabolism), inherited because the superpathway includes folate synthesis downstream of chorismate. Reason: SHMT does not act on chorismate or any chorismate-derived intermediate; this is a superpathway inheritance artifact. Supporting Evidence: file:yeast/SHM1/SHM1-uniprot.txt FUNCTION: Interconversion of serine and glycine. |
| GO:0046653 tetrahydrofolate metabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN000188065 for tetrahydrofolate metabolic process. Reason: Correct (parent of tetrahydrofolate interconversion). Supporting Evidence: PMID:9398220 In Saccharomyces cerevisiae, mitochondrial and cytoplasmic SHMT isozymes are encoded by distinct nuclear genes (SHM1 and SHM2) |
| GO:0046655 folic acid metabolic process | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways RCA from PWY3O-20 (folate polyglutamylation), mapped to folic acid metabolic process. Reason: SHMT neither polyglutamylates folates nor acts on folic acid; within this superpathway its contribution is THF -> 5,10-methylene-THF. The accurate term is tetrahydrofolate interconversion, which the gene already carries. Proposed replacements: tetrahydrofolate interconversion Supporting Evidence: PMID:9398220 In Saccharomyces cerevisiae, mitochondrial and cytoplasmic SHMT isozymes are encoded by distinct nuclear genes (SHM1 and SHM2) |
| GO:0046655 folic acid metabolic process | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways RCA from PWY3O-697 (folate interconversions), mapped to folic acid metabolic process. Reason: The pathway is right but the term is not: SHMT acts on tetrahydrofolate, not on folic acid (pteroylglutamate). The appropriate term is tetrahydrofolate interconversion, which the gene already carries. Proposed replacements: tetrahydrofolate interconversion Supporting Evidence: PMID:9398220 In Saccharomyces cerevisiae, mitochondrial and cytoplasmic SHMT isozymes are encoded by distinct nuclear genes (SHM1 and SHM2) |
Loading supporting content…
Download this section (compressed HTML)Q: Is Shm1 in the matrix exclusively, or is a cytosolic pool produced from alternative translation initiation (UniProt notes erroneous initiation in two submissions)?
Experiment: 13C-serine/glycine tracing in shm1 versus shm2 strains on glycine as nitrogen source to quantify mitochondrial serine synthesis.
Mitochondrial serine hydroxymethyltransferase; converts serine to glycine plus 5,10 methylenetetrahydrofolate; involved in generating precursors for purine, pyrimidine, amino acid, and lipid biosynthesis; reverse reaction generates serine
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)