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Protein

Serine hydroxymethyltransferase, cytosolic

Gene

SHMT1

Organism
Oryctolagus cuniculus (Rabbit)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Interconversion of serine and glycine.1 Publication

Catalytic activityi

5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine.1 Publication

Cofactori

pyridoxal 5'-phosphate1 Publication

Pathwayi: tetrahydrofolate interconversion

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei204 – 2041Nucleophile1 Publication
Active sitei256 – 2561Proton donorBy similarity

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

BRENDAi2.1.2.1. 1749.
UniPathwayiUPA00193.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine hydroxymethyltransferase, cytosolic (EC:2.1.2.11 Publication)
Short name:
SHMT
Alternative name(s):
Glycine hydroxymethyltransferase
Serine methylase
Gene namesi
Name:SHMT1
OrganismiOryctolagus cuniculus (Rabbit)
Taxonomic identifieri9986 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresLagomorphaLeporidaeOryctolagus
Proteomesi
  • UP000001811 Componenti: Unplaced

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved2 Publications
Chaini2 – 484483Serine hydroxymethyltransferase, cytosolicPRO_0000113506Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanine1 Publication
Cross-linki6 ↔ 7Isoaspartyl glycine isopeptide (Asn-Gly); alternate1 Publication
Modified residuei6 – 61Deamidated asparagine; alternate1 Publication
Modified residuei257 – 2571N6-(pyridoxal phosphate)lysine1 Publication

Post-translational modificationi

Deamidation of asparagine produces alternatively aspartate or isoaspartate, which in turn can be converted to aspartate through carboxylmethylation/demethylation.1 Publication

Keywords - PTMi

Acetylation, Isopeptide bond

Proteomic databases

PRIDEiP07511.

Interactioni

Subunit structurei

Homotetramer (PubMed:10387080). 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

Protein-protein interaction databases

STRINGi9986.ENSOCUP00000017814.

Structurei

Secondary structure

1
484
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi18 – 214Combined sources
Beta strandi22 – 243Combined sources
Helixi26 – 294Combined sources
Helixi31 – 4515Combined sources
Beta strandi46 – 494Combined sources
Helixi59 – 657Combined sources
Helixi68 – 703Combined sources
Beta strandi80 – 845Combined sources
Helixi87 – 10317Combined sources
Turni108 – 1103Combined sources
Beta strandi111 – 1144Combined sources
Helixi120 – 13112Combined sources
Beta strandi137 – 1415Combined sources
Helixi143 – 1453Combined sources
Helixi149 – 1513Combined sources
Helixi162 – 1665Combined sources
Beta strandi167 – 1726Combined sources
Turni176 – 1783Combined sources
Beta strandi179 – 1813Combined sources
Helixi183 – 19311Combined sources
Beta strandi196 – 2005Combined sources
Helixi211 – 22010Combined sources
Beta strandi224 – 2285Combined sources
Turni230 – 2323Combined sources
Helixi233 – 2386Combined sources
Helixi244 – 2463Combined sources
Beta strandi249 – 2568Combined sources
Helixi257 – 2593Combined sources
Beta strandi265 – 2706Combined sources
Helixi288 – 2969Combined sources
Turni297 – 3004Combined sources
Helixi306 – 31914Combined sources
Helixi322 – 34423Combined sources
Helixi350 – 3523Combined sources
Beta strandi355 – 3628Combined sources
Helixi363 – 3664Combined sources
Helixi370 – 37910Combined sources
Beta strandi385 – 3873Combined sources
Beta strandi395 – 3973Combined sources
Beta strandi400 – 4045Combined sources
Helixi406 – 4105Combined sources
Helixi415 – 43723Combined sources
Helixi445 – 4539Combined sources
Helixi456 – 47318Combined sources
Beta strandi480 – 4823Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CJ0X-ray2.80A/B15-484[»]
1LS3X-ray2.70A/B/C/D2-484[»]
1RV3X-ray2.40A/B2-484[»]
1RV4X-ray2.95A/B2-484[»]
1RVUX-ray2.50A/B2-484[»]
1RVYX-ray2.90A/B2-484[»]
ProteinModelPortaliP07511.
SMRiP07511. Positions 15-484.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP07511.

Family & Domainsi

Sequence similaritiesi

Belongs to the SHMT family.Curated

Phylogenomic databases

eggNOGiKOG2467. Eukaryota.
COG0112. LUCA.
GeneTreeiENSGT00390000002762.
HOGENOMiHOG000239405.
HOVERGENiHBG002807.
InParanoidiP07511.
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.

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

P07511-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATAVNGAPR DAALWSSHEQ MLAQPLKDSD AEVYDIIKKE SNRQRVGLEL
60 70 80 90 100
IASENFASRA VLEALGSCLN NKYSEGYPGQ RYYGGTEHID ELETLCQKRA
110 120 130 140 150
LQAYGLDPQC WGVNVQPYSG SPANFAVYTA LVEPHGRIMG LDLPDGGHLT
160 170 180 190 200
HGFMTDKKKI SATSIFFESM AYKVNPDTGY IDYDRLEENA RLFHPKLIIA
210 220 230 240 250
GTSCYSRNLD YGRLRKIADE NGAYLMADMA HISGLVVAGV VPSPFEHCHV
260 270 280 290 300
VTTTTHKTLR GCRAGMIFYR RGVRSVDPKT GKEILYNLES LINSAVFPGL
310 320 330 340 350
QGGPHNHAIA GVAVALKQAM TPEFKEYQRQ VVANCRALSA ALVELGYKIV
360 370 380 390 400
TGGSDNHLIL VDLRSKGTDG GRAEKVLEAC SIACNKNTCP GDKSALRPSG
410 420 430 440 450
LRLGTPALTS RGLLEKDFQK VAHFIHRGIE LTVQIQDDTG PRATLKEFKE
460 470 480
KLAGDEKHQR AVRALRQEVE SFAALFPLPG LPGF
Length:484
Mass (Da):52,975
Last modified:January 23, 2007 - v2
Checksum:iC2742A5A8052C5BF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z11846 mRNA. Translation: CAA77870.1.
PIRiS24342. XYRBSC.
RefSeqiNP_001095187.1. NM_001101717.1.
UniGeneiOcu.2076.

Genome annotation databases

EnsembliENSOCUT00000030926; ENSOCUP00000017814; ENSOCUG00000021541.
GeneIDi100009405.
KEGGiocu:100009405.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z11846 mRNA. Translation: CAA77870.1.
PIRiS24342. XYRBSC.
RefSeqiNP_001095187.1. NM_001101717.1.
UniGeneiOcu.2076.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CJ0X-ray2.80A/B15-484[»]
1LS3X-ray2.70A/B/C/D2-484[»]
1RV3X-ray2.40A/B2-484[»]
1RV4X-ray2.95A/B2-484[»]
1RVUX-ray2.50A/B2-484[»]
1RVYX-ray2.90A/B2-484[»]
ProteinModelPortaliP07511.
SMRiP07511. Positions 15-484.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9986.ENSOCUP00000017814.

Proteomic databases

PRIDEiP07511.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSOCUT00000030926; ENSOCUP00000017814; ENSOCUG00000021541.
GeneIDi100009405.
KEGGiocu:100009405.

Organism-specific databases

CTDi6470.

Phylogenomic databases

eggNOGiKOG2467. Eukaryota.
COG0112. LUCA.
GeneTreeiENSGT00390000002762.
HOGENOMiHOG000239405.
HOVERGENiHBG002807.
InParanoidiP07511.
KOiK00600.
OMAiLWSLHEK.
OrthoDBiEOG7327NN.
TreeFamiTF314667.

Enzyme and pathway databases

UniPathwayiUPA00193.
BRENDAi2.1.2.1. 1749.

Miscellaneous databases

EvolutionaryTraceiP07511.

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

  1. "Nucleotide sequence and expression of a cDNA encoding rabbit liver cytosolic serine hydroxymethyltransferase."
    Byrne P.C., Sanders P.G., Snell K.
    Biochem. J. 286:117-123(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY.
    Strain: New Zealand white.
    Tissue: Liver.
  2. "The primary structure of rabbit liver cytosolic serine hydroxymethyltransferase."
    Martini F., Angelaccio S., Pascarella S., Barra D., Bossa F., Schirch V.
    J. Biol. Chem. 262:5499-5509(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-484, ACETYLATION AT ALA-2.
    Tissue: Liver.
  3. "Evidence for the in vivo deamidation and isomerization of an asparaginyl residue in cytosolic serine hydroxymethyltransferase."
    Artigues A., Birkett A., Schirch V.
    J. Biol. Chem. 265:4853-4858(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-15, DEAMIDATION AT ASN-6, ISOPEPTIDE BOND AT ASN-6.
  4. "Evidence for a sulfhydryl group at the active site of serine transhydroxymethylase."
    Schirch L., Slagel S., Barra D., Martini F., Bossa F.
    J. Biol. Chem. 255:2986-2989(1980) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 194-205, ACTIVE SITE CYS-204.
  5. "Crystal structure of rabbit cytosolic serine hydroxymethyltransferase at 2.8-A resolution: mechanistic implications."
    Scarsdale J.N., Kazanina G., Radaev S., Schirch V., Wright H.T.
    Biochemistry 38:8347-8358(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE, COFACTOR, SUBUNIT.
    Strain: New Zealand white.
    Tissue: Liver.

Entry informationi

Entry nameiGLYC_RABIT
AccessioniPrimary (citable) accession number: P07511
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: January 23, 2007
Last modified: May 11, 2016
This is version 136 of the entry and version 2 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. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.