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Protein

Serine hydroxymethyltransferase, mitochondrial

Gene

SHM1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Interconversion of serine and glycine.

Catalytic activityi

5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine.

Cofactori

Pathwayi: tetrahydrofolate interconversion

This protein is involved in the pathway tetrahydrofolate interconversion, which is part of One-carbon metabolism.
View all proteins of this organism that are known to be involved in the pathway tetrahydrofolate interconversion and in One-carbon metabolism.

GO - Molecular functioni

  • glycine hydroxymethyltransferase activity Source: SGD
  • pyridoxal phosphate binding Source: InterPro

GO - Biological processi

  • glycine metabolic process Source: InterPro
  • L-serine metabolic process Source: InterPro
  • one-carbon metabolic process Source: SGD
  • serine family amino acid biosynthetic process Source: SGD
  • tetrahydrofolate interconversion Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

One-carbon metabolism

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BioCyciMetaCyc:YBR263W-MONOMER.
YEAST:YBR263W-MONOMER.
ReactomeiR-SCE-196757. Metabolism of folate and pterines.
R-SCE-71262. Carnitine synthesis.
UniPathwayiUPA00193.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine hydroxymethyltransferase, mitochondrial (EC:2.1.2.1)
Short name:
SHMT
Alternative name(s):
Glycine hydroxymethyltransferase
Serine methylase
Gene namesi
Name:SHM1
Synonyms:SHMT1
Ordered Locus Names:YBR263W
ORF Names:YBR1732
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome II

Organism-specific databases

EuPathDBiFungiDB:YBR263W.
SGDiS000000467. SHM1.

Subcellular locationi

GO - Cellular componenti

  • mitochondrion Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 20MitochondrionSequence analysisAdd BLAST20
ChainiPRO_000003256821 – 490Serine hydroxymethyltransferase, mitochondrialAdd BLAST470

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei265N6-(pyridoxal phosphate)lysineBy similarity1

Proteomic databases

MaxQBiP37292.
PRIDEiP37292.

Interactioni

Subunit structurei

Homotetramer (By similarity). Interacts with NAP1.By similarity1 Publication

Protein-protein interaction databases

BioGridi32958. 37 interactors.
DIPiDIP-4952N.
IntActiP37292. 5 interactors.
MINTiMINT-548725.

Structurei

3D structure databases

ProteinModelPortaliP37292.
SMRiP37292.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the SHMT family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

GeneTreeiENSGT00390000002762.
HOGENOMiHOG000239405.
InParanoidiP37292.
KOiK00600.
OMAiIRSTSCY.
OrthoDBiEOG092C2GWL.

Family and domain databases

CDDicd00378. SHMT. 1 hit.
Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
HAMAPiMF_00051. SHMT. 1 hit.
InterProiIPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
IPR001085. Ser_HO-MeTrfase.
IPR019798. Ser_HO-MeTrfase_PLP_BS.
[Graphical view]
PANTHERiPTHR11680. PTHR11680. 1 hit.
PfamiPF00464. SHMT. 1 hit.
[Graphical view]
PIRSFiPIRSF000412. SHMT. 1 hit.
SUPFAMiSSF53383. SSF53383. 1 hit.
PROSITEiPS00096. SHMT. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P37292-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFPRASALAK CMATVHRRGL LTSGAQSLVS KPVSEGDPEM FDILQQERHR
60 70 80 90 100
QKHSITLIPS ENFTSKAVMD LLGSELQNKY SEGYPGERYY GGNEIIDKSE
110 120 130 140 150
SLCQARALEL YGLDPAKWGV NVQPLSGAPA NLYVYSAIMN VGERLMGLDL
160 170 180 190 200
PDGGHLSHGY QLKSGTPISF ISKYFQSMPY HVDHTTGLID YDNLQVLAKA
210 220 230 240 250
FRPKVIVAGT SAYSRLIDYA RFKEISQGCG AYLMSDMAHI SGLVAANVVP
260 270 280 290 300
SPFEHSDIVT TTTHKSLRGP RGAMIFFRKG IKSVTKKGKE IPYELEKKIN
310 320 330 340 350
FSVFPGHQGG PHNHTIGAMA VALKQAMSPE FKEYQQKIVD NSKWFAQELT
360 370 380 390 400
KMGYKLVSGG TDNHLIVIDL SGTQVDGARV ETILSALNIA ANKNTIPGDK
410 420 430 440 450
SALFPSGLRI GTPAMTTRGF GREEFSQVAK YIDSAVKLAE NLKTLEPTTK
460 470 480 490
LDARSRLNEF KKLCNESSEV AALSGEISKW VGQYPVPGDI
Length:490
Mass (Da):53,686
Last modified:December 6, 2005 - v2
Checksum:i8DECF1ECD6349450
GO

Sequence cautioni

The sequence CAA49927 differs from that shown. Reason: Erroneous initiation.Curated
The sequence CAA85226 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti72L → S in AAA21024 (PubMed:8132653).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L22528 Genomic DNA. Translation: AAA21024.1.
X70529 Genomic DNA. Translation: CAA49927.1. Different initiation.
Z36131 Genomic DNA. Translation: CAA85226.1. Different initiation.
BK006936 Genomic DNA. Translation: DAA07380.1.
PIRiS29348.
RefSeqiNP_009822.4. NM_001178611.3.

Genome annotation databases

EnsemblFungiiYBR263W; YBR263W; YBR263W.
GeneIDi852565.
KEGGisce:YBR263W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L22528 Genomic DNA. Translation: AAA21024.1.
X70529 Genomic DNA. Translation: CAA49927.1. Different initiation.
Z36131 Genomic DNA. Translation: CAA85226.1. Different initiation.
BK006936 Genomic DNA. Translation: DAA07380.1.
PIRiS29348.
RefSeqiNP_009822.4. NM_001178611.3.

3D structure databases

ProteinModelPortaliP37292.
SMRiP37292.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32958. 37 interactors.
DIPiDIP-4952N.
IntActiP37292. 5 interactors.
MINTiMINT-548725.

Proteomic databases

MaxQBiP37292.
PRIDEiP37292.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYBR263W; YBR263W; YBR263W.
GeneIDi852565.
KEGGisce:YBR263W.

Organism-specific databases

EuPathDBiFungiDB:YBR263W.
SGDiS000000467. SHM1.

Phylogenomic databases

GeneTreeiENSGT00390000002762.
HOGENOMiHOG000239405.
InParanoidiP37292.
KOiK00600.
OMAiIRSTSCY.
OrthoDBiEOG092C2GWL.

Enzyme and pathway databases

UniPathwayiUPA00193.
BioCyciMetaCyc:YBR263W-MONOMER.
YEAST:YBR263W-MONOMER.
ReactomeiR-SCE-196757. Metabolism of folate and pterines.
R-SCE-71262. Carnitine synthesis.

Miscellaneous databases

PROiP37292.

Family and domain databases

CDDicd00378. SHMT. 1 hit.
Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
HAMAPiMF_00051. SHMT. 1 hit.
InterProiIPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
IPR001085. Ser_HO-MeTrfase.
IPR019798. Ser_HO-MeTrfase_PLP_BS.
[Graphical view]
PANTHERiPTHR11680. PTHR11680. 1 hit.
PfamiPF00464. SHMT. 1 hit.
[Graphical view]
PIRSFiPIRSF000412. SHMT. 1 hit.
SUPFAMiSSF53383. SSF53383. 1 hit.
PROSITEiPS00096. SHMT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiGLYM_YEAST
AccessioniPrimary (citable) accession number: P37292
Secondary accession number(s): D6VQR0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: December 6, 2005
Last modified: November 30, 2016
This is version 147 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

In eukaryotes there are two forms of the enzymes: a cytosolic one and a mitochondrial one.
Present with 17700 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome II
    Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.