Serine hydroxymethyltransferase, mitochondrial precursor

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P34897 (GLYM_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 125. History...

Clusters with 100%, 90%, 50% identity |

Documents (5) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Serine hydroxymethyltransferase, mitochondrial
Short name=SHMT
EC=2.1.2.1

Alternative name(s):
Glycine hydroxymethyltransferase
Serine methylase

Gene names

Name:

SHMT2

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	504 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Contributes to the de novo mitochondrial thymidylate biosynthesis pathway. Required to prevent uracil accumulation in mtDNA. Interconversion of serine and glycine. Associates with mitochondrial DNA. Ref.8
Catalytic activity	5,10-methylenetetrahydrofolate + glycine + H₂O = tetrahydrofolate + L-serine.
Cofactor	Pyridoxal phosphate.
Pathway	One-carbon metabolism; tetrahydrofolate interconversion.
Subunit structure	Homotetramer.
Subcellular location	Mitochondrion. Mitochondrion matrix › mitochondrion nucleoid. Mitochondrion inner membrane Ref.6 Ref.8.
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 process	One-carbon metabolism
Cellular component	Membrane Mitochondrion Mitochondrion inner membrane Mitochondrion nucleoid
Domain	Transit peptide
Ligand	Pyridoxal phosphate
Molecular function	Methyltransferase Transferase
PTM	Acetylation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Cellular component	microtubule cytoskeleton Inferred from direct assay. Source: HPA mitochondrial inner membrane Inferred from direct assay Ref.8. Source: UniProtKB mitochondrial nucleoid Inferred from direct assay Ref.6. Source: BHF-UCL
Molecular function	chromatin binding Inferred from direct assay Ref.6. Source: UniProtKB glycine hydroxymethyltransferase activity Inferred from direct assay Ref.2. Source: UniProtKB methyltransferase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 29

Mitochondrion

Chain

30 – 504

475

Serine hydroxymethyltransferase, mitochondrial

PRO_0000032562

Amino acid modifications

Modified residue

103

N6-acetyllysine Ref.7

Modified residue

181

N6-acetyllysine Ref.7

Modified residue

196

N6-acetyllysine Ref.7

Modified residue

269

N6-acetyllysine Ref.7

Modified residue

280

N6-(pyridoxal phosphate)lysine By similarity

Modified residue

297

N6-acetyllysine Ref.7

Modified residue

356

N6-acetyllysine Ref.7

Modified residue

464

N6-acetyllysine Ref.7

Modified residue

469

N6-acetyllysine Ref.7

Modified residue

474

N6-acetyllysine Ref.7

Experimental info

Sequence conflict

308

P → L in AAA63258. Ref.2

Secondary structure

504

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P34897 [UniParc].

Last modified May 30, 2000. Version 3.
Checksum: 7A13AF741C68FFD6
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FASTA

504

55,993

        10         20         30         40         50         60 
MLYFSLFWAA RPLQRCGQLV RMAIRAQHSN AAQTQTGEAN RGWTGQESLS DSDPEMWELL 

        70         80         90        100        110        120 
QREKDRQCRG LELIASENFC SRAALEALGS CLNNKYSEGY PGKRYYGGAE VVDEIELLCQ 

       130        140        150        160        170        180 
RRALEAFDLD PAQWGVNVQP YSGSPANLAV YTALLQPHDR IMGLDLPDGG HLTHGYMSDV 

       190        200        210        220        230        240 
KRISATSIFF ESMPYKLNPK TGLIDYNQLA LTARLFRPRL IIAGTSAYAR LIDYARMREV 

       250        260        270        280        290        300 
CDEVKAHLLA DMAHISGLVA AKVIPSPFKH ADIVTTTTHK TLRGARSGLI FYRKGVKAVD 

       310        320        330        340        350        360 
PKTGREIPYT FEDRINFAVF PSLQGGPHNH AIAAVAVALK QACTPMFREY SLQVLKNARA 

       370        380        390        400        410        420 
MADALLERGY SLVSGGTDNH LVLVDLRPKG LDGARAERVL ELVSITANKN TCPGDRSAIT 

       430        440        450        460        470        480 
PGGLRLGAPA LTSRQFREDD FRRVVDFIDE GVNIGLEVKS KTAKLQDFKS FLLKDSETSQ 

       490        500 
RLANLRQRVE QFARAFPMPG FDEH

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Molecular cloning, characterization, and regulation of the human mitochondrial serine hydroxymethyltransferase gene." Stover P.J., Chen L.H., Suh J.R., Stover D.M., Keyomarsi K., Shane B. J. Biol. Chem. 272:1842-1848(1997) [PubMed: 8999870] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 22-504.
[2]	"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] OF 31-504.
[3]	"Cloning of human full-length CDSs in BD Creator(TM) system donor vector." Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A. Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[4]	"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]. Tissue: Muscle, Ovary and Uterus.
[5]	"The genetic organization and protein crystallographic structure of human serine hydroxymethyltransferase." Snell K., Baumann U., Byrne P.C., Chave K.J., Renwick S.B., Sanders P.G., Whitehouse S.K. Adv. Enzyme Regul. 40:353-403(2000) [PubMed: 10828359] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-35.
[6]	"The layered structure of human mitochondrial DNA nucleoids." Bogenhagen D.F., Rousseau D., Burke S. J. Biol. Chem. 283:3665-3675(2008) [PubMed: 18063578] [Abstract] Cited for: SUBCELLULAR LOCATION, ASSOCIATION WITH MITOCHONDRIAL DNA, IDENTIFICATION BY MASS SPECTROMETRY.
[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-103; LYS-181; LYS-196; LYS-269; LYS-297; LYS-356; LYS-464; LYS-469 AND LYS-474, MASS SPECTROMETRY.
[8]	"Identification of a de novo thymidylate biosynthesis pathway in mammalian mitochondria." Anderson D.D., Quintero C.M., Stover P.J. Proc. Natl. Acad. Sci. U.S.A. 108:15163-15168(2011) [PubMed: 21876188] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[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: 21269460] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]	"Crystal structure of human mitochondrial serine hydroxymethyltransferase 2." Structural genomics consortium (SGC) Submitted (OCT-2010) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (2.04 ANGSTROMS) OF 17-504.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U23143 Genomic DNA. Translation: AAA64572.1.
L11932 mRNA. Translation: AAA63258.1.
BT006866 mRNA. Translation: AAP35512.1.
BC011911 mRNA. Translation: AAH11911.1.
BC013677 mRNA. Translation: AAH13677.1.
BC044211 mRNA. Translation: AAH44211.1.
Y12331 Genomic DNA. Translation: CAA72999.1.

IPI

IPI00002520.

PIR

B46746.

RefSeq

NP_001159829.1. NM_001166357.1.
NP_001159830.1. NM_001166358.1.
NP_001159831.1. NM_001166359.1.
NP_005403.2. NM_005412.5.

UniGene

Hs.728151.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3OU5	X-ray	2.04	A	17-504	[»]

ProteinModelPortal

P34897.

SMR

P34897. Positions 42-504.

ModBase

Search...

Protein-protein interaction databases

IntAct

P34897. 14 interactions.

STRING

P34897.

PTM databases

PhosphoSite

P34897.

Polymorphism databases

DMDM

6226865.

Proteomic databases

PRIDE

P34897.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000328923; ENSP00000333667; ENSG00000182199.

GeneID

6472.

KEGG

hsa:6472.

NMPDR

fig|9606.3.peg.7787.

UCSC

uc001snf.1. human.

Organism-specific databases

CTD

6472.

GeneCards

GC12P057623.

H-InvDB

HIX0023234.

HGNC

HGNC:10852. SHMT2.

HPA

HPA020543.
HPA020549.

MIM

138450. gene.

neXtProt

NX_P34897.

GenAtlas

Search...

Phylogenomic databases

eggNOG

prNOG19371.

HOVERGEN

HBG002807.

InParanoid

P34897.

PhylomeDB

P34897.

Gene expression databases

ArrayExpress

P34897.

Bgee

P34897.

CleanEx

HS_SHMT2.

Genevestigator

P34897.

GermOnline

ENSG00000182199. Homo sapiens.

Family and domain databases

InterPro

IPR015424. 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]

Gene3D

G3DSA:3.40.640.10. PyrdxlP-dep_Trfase_major_sub1. 1 hit.
G3DSA:3.90.1150.10. PyrdxlP-dep_Trfase_major_sub2. 1 hit.

K00600.

PANTHER

PTHR11680. Gly_HO-Metrfase. 1 hit.

Pfam

PF00464. SHMT. 1 hit.
[Graphical view]

PIRSF

PIRSF000412. SHMT. 1 hit.

SUPFAM

SSF53383. PyrdxlP-dep_Trfase_major. 1 hit.

PROSITE

PS00096. SHMT. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

DrugBank

DB00145. Glycine.
DB00114. Pyridoxal Phosphate.
DB00116. Tetrahydrofolic acid.

NextBio

25141.

SOURCE

Search...

Entry information

Entry name

GLYM_HUMAN

Accession

Primary (citable) accession number: P34897
Secondary accession number(s): O00740

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	May 30, 2000
Last modified:	January 25, 2012
This is version 125 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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 12

Human chromosome 12: entries, gene names and cross-references to MIM

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

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

PTM databases

Polymorphism databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents