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Protein

Serine hydroxymethyltransferase, cytosolic

Gene

Shmt1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Interconversion of serine and glycine.By similarity

Catalytic activityi

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

Cofactori

pyridoxal 5'-phosphate1 Publication

Pathwayi: tetrahydrofolate interconversion

This protein is involved in the pathway tetrahydrofolate interconversion, which is part of One-carbon metabolism.By similarity
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

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

One-carbon metabolism

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

ReactomeiR-MMU-196757. Metabolism of folate and pterines.
R-MMU-71262. Carnitine synthesis.
UniPathwayiUPA00193.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine hydroxymethyltransferase, cytosolic (EC:2.1.2.1By similarity)
Short name:
SHMT
Alternative name(s):
Glycine hydroxymethyltransferase
Serine methylase
Gene namesi
Name:Shmt1
Synonyms:Shmt
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 11

Organism-specific databases

MGIiMGI:98299. Shmt1.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: MGI
  • cytosol Source: UniProtKB
  • extracellular exosome Source: MGI
  • mitochondrion Source: MGI
  • nucleus Source: BHF-UCL
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Chemistry

ChEMBLiCHEMBL4396.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 478478Serine hydroxymethyltransferase, cytosolicPRO_0000113505Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei251 – 2511N6-(pyridoxal phosphate)lysine1 Publication

Proteomic databases

EPDiP50431.
MaxQBiP50431.
PaxDbiP50431.
PeptideAtlasiP50431.
PRIDEiP50431.

2D gel databases

REPRODUCTION-2DPAGEP50431.
SWISS-2DPAGEP50431.

PTM databases

iPTMnetiP50431.
PhosphoSiteiP50431.
SwissPalmiP50431.

Expressioni

Gene expression databases

BgeeiP50431.
CleanExiMM_SHMT1.
ExpressionAtlasiP50431. baseline and differential.
GenevisibleiP50431. MM.

Interactioni

Subunit structurei

Homotetramer (PubMed:11063567). Identified in complex with FAM175B and the other subunits of the BRISC complex, at least composed of FAM175B/ABRO1, BRCC3/BRCC36, BRE/BRCC45 and BABAM1/NBA1.By similarity1 Publication

GO - Molecular functioni

Protein-protein interaction databases

IntActiP50431. 2 interactions.
MINTiMINT-1869579.
STRINGi10090.ENSMUSP00000018744.

Structurei

Secondary structure

1
478
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 53Combined sources
Helixi6 – 1510Combined sources
Helixi20 – 234Combined sources
Helixi25 – 3915Combined sources
Beta strandi40 – 434Combined sources
Helixi53 – 597Combined sources
Helixi62 – 654Combined sources
Beta strandi72 – 743Combined sources
Beta strandi76 – 783Combined sources
Helixi81 – 9717Combined sources
Turni102 – 1043Combined sources
Beta strandi105 – 1084Combined sources
Helixi114 – 12512Combined sources
Beta strandi131 – 1355Combined sources
Helixi137 – 1393Combined sources
Helixi143 – 1453Combined sources
Helixi156 – 1605Combined sources
Beta strandi161 – 1666Combined sources
Turni170 – 1723Combined sources
Helixi177 – 18711Combined sources
Beta strandi190 – 1945Combined sources
Helixi205 – 21410Combined sources
Beta strandi218 – 2225Combined sources
Helixi224 – 2263Combined sources
Helixi227 – 2315Combined sources
Helixi238 – 2403Combined sources
Beta strandi243 – 2508Combined sources
Helixi251 – 2533Combined sources
Beta strandi259 – 2646Combined sources
Beta strandi266 – 2705Combined sources
Beta strandi277 – 2804Combined sources
Helixi282 – 2909Combined sources
Turni291 – 2944Combined sources
Helixi300 – 31314Combined sources
Helixi316 – 33823Combined sources
Beta strandi349 – 3568Combined sources
Helixi357 – 3604Combined sources
Helixi364 – 37310Combined sources
Beta strandi384 – 3874Combined sources
Beta strandi393 – 3986Combined sources
Helixi400 – 4034Combined sources
Turni404 – 4063Combined sources
Helixi409 – 43123Combined sources
Helixi439 – 4479Combined sources
Helixi453 – 46715Combined sources
Beta strandi474 – 4763Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EJIX-ray2.90A/B/C/D1-478[»]
ProteinModelPortaliP50431.
SMRiP50431. Positions 1-478.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP50431.

Family & Domainsi

Sequence similaritiesi

Belongs to the SHMT family.Curated

Phylogenomic databases

eggNOGiKOG2467. Eukaryota.
COG0112. LUCA.
GeneTreeiENSGT00390000002762.
HOGENOMiHOG000239405.
HOVERGENiHBG002807.
InParanoidiP50431.
KOiK00600.
OMAiLWSLHEK.
OrthoDBiEOG7327NN.
TreeFamiTF314667.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
HAMAPiMF_00051. SHMT.
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.

P50431-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MADRDATLWA SHEKMLSQPL KDSDAEVYSI IKKESNRQRV GLELIASENF
60 70 80 90 100
ASRAVLEALG SCLNNKYSEG YPGQRYYGGT EFIDELEMLC QKRALQAYHL
110 120 130 140 150
DPQCWGVNVQ PYSGSPANFA VYTALVEPHG RIMGLDLPDG GHLTHGFMTD
160 170 180 190 200
KKKISATSIF FESMPYKVYP ETGYINYDQL EENASLFHPK LIIAGTSCYS
210 220 230 240 250
RNLDYARLRK IADDNGAYLM ADMAHISGLV AAGVVPSPFE HCHVVTTTTH
260 270 280 290 300
KTLRGCRAGM IFYRKGVRSV DPKTGKETYY ELESLINSAV FPGLQGGPHN
310 320 330 340 350
HAIAGVAVAL KQAMTTEFKI YQLQVLANCR ALSDALTELG YKIVTGGSDN
360 370 380 390 400
HLILMDLRSK GTDGGRAEKV LEACSIACNK NTCPGDKSAL RPSGLRLGTP
410 420 430 440 450
ALTSRGLLEE DFQKVAHFIH RGIELTLQIQ SHMATKATLK EFKEKLAGDE
460 470
KIQSAVATLR EEVENFASNF SLPGLPDF
Length:478
Mass (Da):52,601
Last modified:July 27, 2011 - v3
Checksum:i780C764C5AA3CEA3
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti62 – 621C → S in AAK15040 (PubMed:11063567).Curated
Sequence conflicti62 – 621C → S in CAA64225 (PubMed:8863732).Curated
Sequence conflicti62 – 621C → S in CAA64226 (PubMed:8863732).Curated
Sequence conflicti267 – 30943VRSVD…GVAVA → KFPYAGTDSVGSHFLCGRDW ENSGLSLLGKIGALALEELL RKK in CAA64225 (PubMed:8863732).CuratedAdd
BLAST
Sequence conflicti304 – 3041A → R in CAA64226 (PubMed:8863732).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF237702 mRNA. Translation: AAK15040.1.
AL596215 Genomic DNA. Translation: CAI35264.1.
BC026055 mRNA. Translation: AAH26055.1.
X94478 mRNA. Translation: CAA64225.1.
X94479 mRNA. Translation: CAA64226.1.
CCDSiCCDS24799.1.
PIRiJC4959.
RefSeqiNP_033197.2. NM_009171.2.
XP_006532707.1. XM_006532644.2.
UniGeneiMm.364956.

Genome annotation databases

EnsembliENSMUST00000018744; ENSMUSP00000018744; ENSMUSG00000020534.
GeneIDi20425.
KEGGimmu:20425.
UCSCiuc007jgo.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF237702 mRNA. Translation: AAK15040.1.
AL596215 Genomic DNA. Translation: CAI35264.1.
BC026055 mRNA. Translation: AAH26055.1.
X94478 mRNA. Translation: CAA64225.1.
X94479 mRNA. Translation: CAA64226.1.
CCDSiCCDS24799.1.
PIRiJC4959.
RefSeqiNP_033197.2. NM_009171.2.
XP_006532707.1. XM_006532644.2.
UniGeneiMm.364956.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EJIX-ray2.90A/B/C/D1-478[»]
ProteinModelPortaliP50431.
SMRiP50431. Positions 1-478.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP50431. 2 interactions.
MINTiMINT-1869579.
STRINGi10090.ENSMUSP00000018744.

Chemistry

ChEMBLiCHEMBL4396.

PTM databases

iPTMnetiP50431.
PhosphoSiteiP50431.
SwissPalmiP50431.

2D gel databases

REPRODUCTION-2DPAGEP50431.
SWISS-2DPAGEP50431.

Proteomic databases

EPDiP50431.
MaxQBiP50431.
PaxDbiP50431.
PeptideAtlasiP50431.
PRIDEiP50431.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000018744; ENSMUSP00000018744; ENSMUSG00000020534.
GeneIDi20425.
KEGGimmu:20425.
UCSCiuc007jgo.1. mouse.

Organism-specific databases

CTDi6470.
MGIiMGI:98299. Shmt1.

Phylogenomic databases

eggNOGiKOG2467. Eukaryota.
COG0112. LUCA.
GeneTreeiENSGT00390000002762.
HOGENOMiHOG000239405.
HOVERGENiHBG002807.
InParanoidiP50431.
KOiK00600.
OMAiLWSLHEK.
OrthoDBiEOG7327NN.
TreeFamiTF314667.

Enzyme and pathway databases

UniPathwayiUPA00193.
ReactomeiR-MMU-196757. Metabolism of folate and pterines.
R-MMU-71262. Carnitine synthesis.

Miscellaneous databases

EvolutionaryTraceiP50431.
PROiP50431.
SOURCEiSearch...

Gene expression databases

BgeeiP50431.
CleanExiMM_SHMT1.
ExpressionAtlasiP50431. baseline and differential.
GenevisibleiP50431. MM.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
HAMAPiMF_00051. SHMT.
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...

Publicationsi

« Hide 'large scale' publications
  1. "Structure of a murine cytoplasmic serine hydroxymethyltransferase quinonoid ternary complex: evidence for asymmetric obligate dimers."
    Szebenyi D.M.E., Liu X., Kriksunov I.A., Stover P.J., Thiel D.J.
    Biochemistry 39:13313-13323(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE AND SUBSTRATES, COFACTOR, SUBUNIT.
    Strain: 129/Sv.
    Tissue: Liver.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: FVB/N.
    Tissue: Liver.
  4. "Isolation of retinoic acid-repressed genes from P19 embryonal carcinoma cells."
    Nakshatri H., Bouillet P., Bhat-Nakshatri P., Chambon P.
    Gene 174:79-84(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-316.
  5. Lubec G., Sunyer B., Chen W.-Q.
    Submitted (JAN-2009) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 22-32; 40-53; 331-342 AND 452-460, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: OF1.
    Tissue: Hippocampus.
  6. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brown adipose tissue, Kidney, Liver, Pancreas, Spleen and Testis.

Entry informationi

Entry nameiGLYC_MOUSE
AccessioniPrimary (citable) accession number: P50431
Secondary accession number(s): Q64508, Q8R0X9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: July 27, 2011
Last modified: July 6, 2016
This is version 142 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

In eukaryotes there are two forms of the enzymes: a cytosolic one and a mitochondrial one.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

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.