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P34896 (GLYC_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 151. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (7) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Serine hydroxymethyltransferase, cytosolic

Short name=SHMT
EC=2.1.2.1
Alternative name(s):
Glycine hydroxymethyltransferase
Serine methylase
Gene names
Name:SHMT1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length483 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Interconversion of serine and glycine. HAMAP-Rule MF_00051

Catalytic activity

5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine. HAMAP-Rule MF_00051

Cofactor

Pyridoxal phosphate.

Pathway

One-carbon metabolism; tetrahydrofolate interconversion. HAMAP-Rule MF_00051

Subunit structure

Homotetramer.

Subcellular location

Cytoplasm HAMAP-Rule MF_00051.

Miscellaneous

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

Sequence similarities

Belongs to the SHMT family.

Ontologies

Keywords
   Biological processOne-carbon metabolism
   Cellular componentCytoplasm
   Coding sequence diversityAlternative splicing
Polymorphism
   LigandPyridoxal phosphate
   Molecular functionTransferase
   PTMAcetylation
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processL-serine catabolic process

Inferred from direct assay PubMed 17482557. Source: UniProtKB

carnitine biosynthetic process

Traceable author statement. Source: Reactome

cellular nitrogen compound metabolic process

Traceable author statement. Source: Reactome

folic acid metabolic process

Inferred from direct assay PubMed 11278996. Source: UniProtKB

glycine biosynthetic process from serine

Inferred from electronic annotation. Source: Ensembl

protein homotetramerization

Inferred from electronic annotation. Source: Ensembl

protein tetramerization

Inferred from direct assay Ref.10. Source: UniProtKB

purine nucleobase biosynthetic process

Inferred from direct assay PubMed 11516159. Source: UniProtKB

small molecule metabolic process

Traceable author statement. Source: Reactome

tetrahydrofolate interconversion

Inferred from electronic annotation. Source: UniProtKB-UniPathway

vitamin metabolic process

Traceable author statement. Source: Reactome

water-soluble vitamin metabolic process

Traceable author statement. Source: Reactome

   Cellular_componentcytoplasm

Inferred from direct assay. Source: HPA

cytosol

Inferred from direct assay PubMed 17482557. Source: UniProtKB

extracellular vesicular exosome

Inferred from direct assay PubMed 19056867PubMed 23376485. Source: UniProt

mitochondrion

Inferred from electronic annotation. Source: Ensembl

nucleus

Inferred from direct assay. Source: HPA

   Molecular_functionL-allo-threonine aldolase activity

Inferred from electronic annotation. Source: Ensembl

amino acid binding

Inferred from electronic annotation. Source: Ensembl

glycine hydroxymethyltransferase activity

Inferred from direct assay PubMed 17482557Ref.1. Source: UniProtKB

protein homodimerization activity

Inferred from direct assay Ref.10. Source: UniProtKB

pyridoxal phosphate binding

Inferred from direct assay PubMed 17482557. Source: UniProtKB

Complete GO annotation...

Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: P34896-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: P34896-2)

The sequence of this isoform differs from the canonical sequence as follows:
     274-312: Missing.
Note: Contains a N6-acetyllysine at position 271.
Isoform 3 (identifier: P34896-3)

The sequence of this isoform differs from the canonical sequence as follows:
     273-352: Missing.
Isoform 4 (identifier: P34896-4)

The sequence of this isoform differs from the canonical sequence as follows:
     1-138: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed By similarity
Chain2 – 483482Serine hydroxymethyltransferase, cytosolic HAMAP-Rule MF_00051
PRO_0000113504

Amino acid modifications

Modified residue2571N6-(pyridoxal phosphate)lysine HAMAP-Rule MF_00051

Natural variations

Alternative sequence1 – 138138Missing in isoform 4.
VSP_054610
Alternative sequence273 – 35280Missing in isoform 3.
VSP_006096
Alternative sequence274 – 31239Missing in isoform 2.
VSP_006095
Natural variant3401E → Q.
Corresponds to variant rs7215148 [ dbSNP | Ensembl ].
VAR_059795
Natural variant4741L → F. Ref.6 Ref.7
Corresponds to variant rs1979277 [ dbSNP | Ensembl ].
VAR_022010

Secondary structure

................................................................................. 483
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified February 1, 1994. Version 1.
Checksum: 6CDD6CA06D017C19

FASTA48353,083
        10         20         30         40         50         60 
MTMPVNGAHK DADLWSSHDK MLAQPLKDSD VEVYNIIKKE SNRQRVGLEL IASENFASRA 

        70         80         90        100        110        120 
VLEALGSCLN NKYSEGYPGQ RYYGGTEFID ELETLCQKRA LQAYKLDPQC WGVNVQPYSG 

       130        140        150        160        170        180 
SPANFAVYTA LVEPHGRIMG LDLPDGGHLT HGFMTDKKKI SATSIFFESM PYKVNPDTGY 

       190        200        210        220        230        240 
INYDQLEENA RLFHPKLIIA GTSCYSRNLE YARLRKIADE NGAYLMADMA HISGLVAAGV 

       250        260        270        280        290        300 
VPSPFEHCHV VTTTTHKTLR GCRAGMIFYR KGVKSVDPKT GKEILYNLES LINSAVFPGL 

       310        320        330        340        350        360 
QGGPHNHAIA GVAVALKQAM TLEFKVYQHQ VVANCRALSE ALTELGYKIV TGGSDNHLIL 

       370        380        390        400        410        420 
VDLRSKGTDG GRAEKVLEAC SIACNKNTCP GDRSALRPSG LRLGTPALTS RGLLEKDFQK 

       430        440        450        460        470        480 
VAHFIHRGIE LTLQIQSDTG VRATLKEFKE RLAGDKYQAA VQALREEVES FASLFPLPGL 


PDF 

« Hide

Isoform 2 [UniParc].

Checksum: 92091DCEB64B65D1
Show »

FASTA44449,028
Isoform 3 [UniParc].

Checksum: 9CE930DFA6FC1FF7
Show »

FASTA40344,552
Isoform 4 [UniParc].

Checksum: DD683D88B3A1D1FA
Show »

FASTA34537,672

References

« Hide 'large scale' references
[1]"Cloning of human cDNAs encoding mitochondrial and cytosolic serine hydroxymethyltransferases and chromosomal localization."
Garrow T.A., Brenner A.A., Whitehead M.V., Chen X.-N., Duncan R.G., Korenberg J.R., Shane B.
J. Biol. Chem. 268:11910-11916(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]Xu L., Mangum J.H., Robertson D.L.
Submitted (JAN-1994) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
Tissue: Liver.
[3]"Isolation and characterisation of human genomic sequences encoding cytosolic serine hydroxymethyltransferase."
Chave K.J., Snell K., Sanders P.G.
Biochem. Soc. Trans. 25:53-53(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
Tissue: Mammary gland.
[4]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4).
Tissue: Liver.
[5]"DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage."
Zody M.C., Garber M., Adams D.J., Sharpe T., Harrow J., Lupski J.R., Nicholson C., Searle S.M., Wilming L., Young S.K., Abouelleil A., Allen N.R., Bi W., Bloom T., Borowsky M.L., Bugalter B.E., Butler J., Chang J.L. expand/collapse author list , Chen C.-K., Cook A., Corum B., Cuomo C.A., de Jong P.J., DeCaprio D., Dewar K., FitzGerald M., Gilbert J., Gibson R., Gnerre S., Goldstein S., Grafham D.V., Grocock R., Hafez N., Hagopian D.S., Hart E., Norman C.H., Humphray S., Jaffe D.B., Jones M., Kamal M., Khodiyar V.K., LaButti K., Laird G., Lehoczky J., Liu X., Lokyitsang T., Loveland J., Lui A., Macdonald P., Major J.E., Matthews L., Mauceli E., McCarroll S.A., Mihalev A.H., Mudge J., Nguyen C., Nicol R., O'Leary S.B., Osoegawa K., Schwartz D.C., Shaw-Smith C., Stankiewicz P., Steward C., Swarbreck D., Venkataraman V., Whittaker C.A., Yang X., Zimmer A.R., Bradley A., Hubbard T., Birren B.W., Rogers J., Lander E.S., Nusbaum C.
Nature 440:1045-1049(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], VARIANT PHE-474.
[7]"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] (ISOFORMS 1 AND 2), VARIANT PHE-474.
Tissue: Bone marrow, Lymph and Testis.
[8]"Lysine acetylation targets protein complexes and co-regulates major cellular functions."
Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-271 (ISOFORM 2), IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[9]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]"The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy."
Renwick S.B., Snell K., Baumann U.
Structure 6:1105-1116(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS) OF 11-480.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
L11931 mRNA. Translation: AAA63257.1.
L23928 mRNA. Translation: AAA36020.1.
L23928 mRNA. Translation: AAA36019.1.
L23928 mRNA. Translation: AAA36018.1.
Y14485 mRNA. Translation: CAB54838.1.
Y14486 mRNA. Translation: CAB54839.1.
Y14487 mRNA. Translation: CAB54840.1.
AK298415 mRNA. Translation: BAG60641.1.
AC127537 Genomic DNA. No translation available.
AL353997 Genomic DNA. No translation available.
CH471196 Genomic DNA. Translation: EAW55637.1.
CH471196 Genomic DNA. Translation: EAW55640.1.
CH471196 Genomic DNA. Translation: EAW55641.1.
BC007979 mRNA. Translation: AAH07979.1.
BC022874 mRNA. Translation: AAH22874.1.
BC038598 mRNA. Translation: AAH38598.1.
CCDSCCDS11196.1. [P34896-1]
CCDS11197.1. [P34896-2]
PIRA46746.
RefSeqNP_001268715.1. NM_001281786.1. [P34896-4]
NP_004160.3. NM_004169.4. [P34896-1]
NP_683718.1. NM_148918.2. [P34896-2]
XP_005256824.1. XM_005256767.1. [P34896-1]
UniGeneHs.513987.
Hs.592944.
Hs.636044.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1BJ4X-ray2.65A11-480[»]
ProteinModelPortalP34896.
SMRP34896. Positions 11-480.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid112366. 34 interactions.
IntActP34896. 5 interactions.
STRING9606.ENSP00000318868.

Chemistry

BindingDBP34896.
ChEMBLCHEMBL1772927.
DrugBankDB00145. Glycine.
DB01055. Mimosine.
DB00114. Pyridoxal Phosphate.
DB00116. Tetrahydrofolic acid.

PTM databases

PhosphoSiteP34896.

Polymorphism databases

DMDM462184.

Proteomic databases

MaxQBP34896.
PaxDbP34896.
PRIDEP34896.

Protocols and materials databases

DNASU6470.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000316694; ENSP00000318868; ENSG00000176974. [P34896-1]
ENST00000352886; ENSP00000345881; ENSG00000176974. [P34896-3]
ENST00000354098; ENSP00000318805; ENSG00000176974. [P34896-2]
ENST00000539052; ENSP00000440089; ENSG00000176974.
GeneID6470.
KEGGhsa:6470.
UCSCuc002gsz.3. human. [P34896-1]
uc002gtb.3. human. [P34896-2]

Organism-specific databases

CTD6470.
GeneCardsGC17M018231.
HGNCHGNC:10850. SHMT1.
HPAHPA023314.
MIM182144. gene.
neXtProtNX_P34896.
PharmGKBPA35753.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG0112.
HOGENOMHOG000239405.
HOVERGENHBG002807.
InParanoidP34896.
KOK00600.
OMAQAMTLEF.
OrthoDBEOG7327NN.
PhylomeDBP34896.
TreeFamTF314667.

Enzyme and pathway databases

BioCycMetaCyc:HS11114-MONOMER.
ReactomeREACT_111217. Metabolism.
REACT_116125. Disease.
UniPathwayUPA00193.

Gene expression databases

ArrayExpressP34896.
BgeeP34896.
CleanExHS_SHMT1.
GenevestigatorP34896.

Family and domain databases

Gene3D3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
HAMAPMF_00051. SHMT.
InterProIPR015424. 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]
PANTHERPTHR11680. PTHR11680. 1 hit.
PfamPF00464. SHMT. 1 hit.
[Graphical view]
PIRSFPIRSF000412. SHMT. 1 hit.
SUPFAMSSF53383. SSF53383. 1 hit.
PROSITEPS00096. SHMT. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSSHMT1. human.
EvolutionaryTraceP34896.
GenomeRNAi6470.
NextBio25133.
PROP34896.
SOURCESearch...

Entry information

Entry nameGLYC_HUMAN
AccessionPrimary (citable) accession number: P34896
Secondary accession number(s): B4DPM9 expand/collapse secondary AC list , D3DXD0, Q96HY0, Q9UMD1, Q9UMD2
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: February 1, 1994
Last modified: July 9, 2014
This is version 151 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 17

Human chromosome 17: entries, gene names and cross-references to MIM