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P34896 (GLYC_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 126. 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
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)
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length483 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Interconversion of serine and glycine.

Catalytic activity

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

Cofactor

Pyridoxal phosphate.

Pathway

One-carbon metabolism; tetrahydrofolate interconversion.

Subunit structure

Homotetramer.

Subcellular location

Cytoplasm.

Miscellaneous

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

Sequence similarities

Belongs to the SHMT family.

Alternative products

This entry describes 3 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.
Isoform 3 (identifier: P34896-3)

The sequence of this isoform differs from the canonical sequence as follows:
     273-352: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 483483Serine hydroxymethyltransferase, cytosolic
PRO_0000113504

Amino acid modifications

Modified residue341Phosphotyrosine Ref.6
Modified residue2571N6-(pyridoxal phosphate)lysine
Modified residue2711N6-acetyllysine Ref.7

Natural variations

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.4 Ref.5
Corresponds to variant rs1979277 [ dbSNP | Ensembl ].
VAR_022010

Secondary structure

1 ................................................................................. 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

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: 8505317] [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: 9056951] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
Tissue: Mammary gland.
[4]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.
[5]"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: 15489334] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2), VARIANT PHE-474.
Tissue: Bone marrow, Lymph and Testis.
[6]"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
Sci. Signal. 2:RA46-RA46(2009) [PubMed: 19690332] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-34, MASS SPECTROMETRY.
Tissue: Leukemic T-cell.
[7]"Lysine acetylation targets protein complexes and co-regulates major cellular functions."
Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T., Olsen J.V., Mann M.
Science 325:834-840(2009) [PubMed: 19608861] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-271, MASS SPECTROMETRY.
[8]"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: 21269460] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[9]"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: 9753690] [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.
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.
IPIIPI00002519.
IPI00220668.
IPI00220669.
PIRA46746.
RefSeqNP_004160.3. NM_004169.3.
NP_683718.1. NM_148918.1.
UniGeneHs.513987.
Hs.636044.

3D structure databases

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

Protein-protein interaction databases

IntActP34896. 5 interactions.
STRINGP34896.

PTM databases

PhosphoSiteP34896.

Polymorphism databases

DMDM462184.

Proteomic databases

PRIDEP34896.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000316694; ENSP00000318868; ENSG00000176974.
GeneID6470.
KEGGhsa:6470.
NMPDRfig|9606.3.peg.13247.
UCSCuc002gta.1. human.
uc002gtb.1. human.

Organism-specific databases

CTD6470.
GeneCardsGC17M018171.
H-InvDBHIX0013601.
HGNCHGNC:10850. SHMT1.
HPAHPA023314.
MIM182144. gene.
neXtProtNX_P34896.
PharmGKBPA35753.
GenAtlasSearch...

Phylogenomic databases

eggNOGprNOG14595.
HOGENOMHBG301263.
HOVERGENHBG002807.
InParanoidP34896.
OMAEFKVYQH.
OrthoDBEOG42Z4Q2.
PhylomeDBP34896.

Enzyme and pathway databases

ReactomeREACT_111217. Metabolism.

Gene expression databases

ArrayExpressP34896.
BgeeP34896.
CleanExHS_SHMT1.
GenevestigatorP34896.
GermOnlineENSG00000176974. Homo sapiens.

Family and domain databases

InterProIPR015424. PyrdxlP-dep_Trfase_major_dom.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
IPR001085. Ser_HO-MeTrfase.
IPR019798. Ser_HO-MeTrfase_PLP_BS.
[Graphical view]
Gene3DG3DSA:3.40.640.10. PyrdxlP-dep_Trfase_major_sub1. 1 hit.
G3DSA:3.90.1150.10. PyrdxlP-dep_Trfase_major_sub2. 1 hit.
KOK00600.
PANTHERPTHR11680. Gly_HO-Metrfase. 1 hit.
PfamPF00464. SHMT. 1 hit.
[Graphical view]
PIRSFPIRSF000412. SHMT. 1 hit.
SUPFAMSSF53383. PyrdxlP-dep_Trfase_major. 1 hit.
PROSITEPS00096. SHMT. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

DrugBankDB00145. Glycine.
DB01055. Mimosine.
DB00114. Pyridoxal Phosphate.
DB00116. Tetrahydrofolic acid.
NextBio25133.
SOURCESearch...

Entry information

Entry nameGLYC_HUMAN
AccessionPrimary (citable) accession number: P34896
Secondary accession number(s): D3DXD0 expand/collapse secondary AC list , Q96HY0, Q9UMD1, Q9UMD2
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: February 1, 1994
Last modified: January 25, 2012
This is version 126 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

Human chromosome 17

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

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

MIM cross-references

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

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents