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Aliases for SHMT2 Gene

Aliases for SHMT2 Gene

  • Serine Hydroxymethyltransferase 2 2 3
  • Serine Hydroxymethyltransferase 2 (Mitochondrial) 2 3 5
  • Glycine Hydroxymethyltransferase 3 4
  • Serine Methylase 3 4
  • EC 2.1.2.1 4 63
  • SHMT 3 4
  • Epididymis Secretory Sperm Binding Protein Li 51e 3
  • Glycine Auxotroph A, Human Complement For Hamster 3
  • Serine Hydroxymethylase 3
  • Threonine Aldolase 3
  • Serine Aldolase 3
  • HEL-S-51e 3
  • GLY A+ 3
  • GLYA 3

External Ids for SHMT2 Gene

Previous HGNC Symbols for SHMT2 Gene

  • SHMT

Previous GeneCards Identifiers for SHMT2 Gene

  • GC12U990093
  • GC12P057340
  • GC12P055909
  • GC12P055886
  • GC12P057623
  • GC12P054662

Summaries for SHMT2 Gene

Entrez Gene Summary for SHMT2 Gene

  • This gene encodes the mitochondrial form of a pyridoxal phosphate-dependent enzyme that catalyzes the reversible reaction of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. The encoded product is primarily responsible for glycine synthesis. The activity of the encoded protein has been suggested to be the primary source of intracellular glycine. The gene which encodes the cytosolic form of this enzyme is located on chromosome 17. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

GeneCards Summary for SHMT2 Gene

SHMT2 (Serine Hydroxymethyltransferase 2) is a Protein Coding gene. Diseases associated with SHMT2 include pyridoxine deficiency and neural tube defects. Among its related pathways are Metabolism and Carbon metabolism. GO annotations related to this gene include identical protein binding and pyridoxal phosphate binding. An important paralog of this gene is SHMT1.

UniProtKB/Swiss-Prot for SHMT2 Gene

  • Contributes to the de novo mitochondrial thymidylate biosynthesis pathway via its role in glycine and tetrahydrofolate metabolism. Thymidylate biosynthesis is required to prevent uracil accumulation in mtDNA (PubMed:21876188). Interconversion of serine and glycine (PubMed:25619277). Associates with mitochondrial DNA (PubMed:18063578). Plays a role in the deubiquitination of target proteins as component of the BRISC complex (PubMed:24075985). Required for IFNAR1 deubiquitination by the BRISC complex (PubMed:24075985).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SHMT2 Gene

Genomics for SHMT2 Gene

Regulatory Elements for SHMT2 Gene

Promoters for SHMT2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around SHMT2 on UCSC Golden Path with GeneCards custom track

Genomic Location for SHMT2 Gene

Chromosome:
12
Start:
57,229,327 bp from pter
End:
57,234,935 bp from pter
Size:
5,609 bases
Orientation:
Plus strand

Genomic View for SHMT2 Gene

Genes around SHMT2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SHMT2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SHMT2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SHMT2 Gene

Proteins for SHMT2 Gene

  • Protein details for SHMT2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P34897-GLYM_HUMAN
    Recommended name:
    Serine hydroxymethyltransferase, mitochondrial
    Protein Accession:
    P34897
    Secondary Accessions:
    • B7Z9F1
    • E7EQ19
    • E7EU43
    • O00740
    • Q8N1A5

    Protein attributes for SHMT2 Gene

    Size:
    504 amino acids
    Molecular mass:
    55993 Da
    Cofactor:
    Name=pyridoxal 5-phosphate; Xref=ChEBI:CHEBI:597326;
    Quaternary structure:
    • Homotetramer; in the presence of bound pyridoxal 5-phosphate. Homodimer; in the absence of bound pyridoxal 5-phosphate. Pyridoxal 5-phosphate binding mediates an important conformation change that is required for tetramerization (PubMed:25619277). Interacts with FAM175B; the interaction is direct. Identified in a complex with FAM175B and the other subunits of the BRISC complex, at least composed of the FAM175B/ABRO1, BRCC3/BRCC36, BRE/BRCC45 and BABAM1/NBA1. Identified in a complex with FAM175B and INAR1 (PubMed:24075985). Interacts with KIRREL3 (PubMed:25902260).
    Miscellaneous:
    • In eukaryotes there are two forms of the enzymes: a cytosolic one and a mitochondrial one.

    Three dimensional structures from OCA and Proteopedia for SHMT2 Gene

    Alternative splice isoforms for SHMT2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SHMT2 Gene

Proteomics data for SHMT2 Gene at MOPED

Post-translational modifications for SHMT2 Gene

  • Ubiquitination at Lys 95, Lys 409, and Lys 469
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for SHMT2 (SHMT2)
  • Cloud-Clone Corp. Antibodies for SHMT2

Domains & Families for SHMT2 Gene

Graphical View of Domain Structure for InterPro Entry

P34897

UniProtKB/Swiss-Prot:

GLYM_HUMAN :
  • Belongs to the SHMT family.
Family:
  • Belongs to the SHMT family.
genes like me logo Genes that share domains with SHMT2: view

No data available for Gene Families for SHMT2 Gene

Function for SHMT2 Gene

Molecular function for SHMT2 Gene

GENATLAS Biochemistry:
serine hydroxy-methyltransferase,pyridoxal dependent,mitochondrial,catalyzing 5-10 methylene THF synthesis,"one-carbone" metabolism,putative regulator of cell growth and proliferation
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=278 uM for L-serine {ECO:0000269 PubMed:25619277}; KM=23 uM for tetrahydrofolate {ECO:0000269 PubMed:25619277};
UniProtKB/Swiss-Prot CatalyticActivity:
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine.
UniProtKB/Swiss-Prot Function:
Contributes to the de novo mitochondrial thymidylate biosynthesis pathway via its role in glycine and tetrahydrofolate metabolism. Thymidylate biosynthesis is required to prevent uracil accumulation in mtDNA (PubMed:21876188). Interconversion of serine and glycine (PubMed:25619277). Associates with mitochondrial DNA (PubMed:18063578). Plays a role in the deubiquitination of target proteins as component of the BRISC complex (PubMed:24075985). Required for IFNAR1 deubiquitination by the BRISC complex (PubMed:24075985).

Enzyme Numbers (IUBMB) for SHMT2 Gene

Gene Ontology (GO) - Molecular Function for SHMT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding IDA 18063578
GO:0042802 identical protein binding IEA --
genes like me logo Genes that share ontologies with SHMT2: view
genes like me logo Genes that share phenotypes with SHMT2: view

Animal Model Products

  • Taconic Biosciences Mouse Models for SHMT2

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SHMT2 Gene

Localization for SHMT2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SHMT2 Gene

Mitochondrion. Mitochondrion matrix, mitochondrion nucleoid. Mitochondrion inner membrane. Cytoplasm. Nucleus.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SHMT2 Gene COMPARTMENTS Subcellular localization image for SHMT2 gene
Compartment Confidence
cytoskeleton 5
extracellular 5
mitochondrion 5
nucleus 5
cytosol 2
peroxisome 2
chloroplast 1

Gene Ontology (GO) - Cellular Components for SHMT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IDA 17482557
GO:0005743 mitochondrial inner membrane TAS --
genes like me logo Genes that share ontologies with SHMT2: view

Pathways & Interactions for SHMT2 Gene

genes like me logo Genes that share pathways with SHMT2: view

UniProtKB/Swiss-Prot P34897-GLYM_HUMAN

  • Pathway: One-carbon metabolism; tetrahydrofolate interconversion.

Gene Ontology (GO) - Biological Process for SHMT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006544 glycine metabolic process IEA,IGI 19513116
GO:0006564 L-serine biosynthetic process IEA --
GO:0006767 water-soluble vitamin metabolic process TAS --
GO:0019264 glycine biosynthetic process from serine IEA --
GO:0035999 tetrahydrofolate interconversion IEA --
genes like me logo Genes that share ontologies with SHMT2: view

No data available for SIGNOR curated interactions for SHMT2 Gene

Drugs & Compounds for SHMT2 Gene

(10) Drugs for SHMT2 Gene - From: HMDB, DrugBank, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Glycine Approved Nutra Full agonist, Agonist, Target, Target Endogenous potentiator, co-transmitter 94
Tetrahydrofolic acid Approved Nutra Target, Target, cofactor 0
L-Serine Approved Nutra Full agonist, Agonist 0
Pyridoxal Phosphate Nutra Target, Target, cofactor 14

(10) Additional Compounds for SHMT2 Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
5,10-Methylenetetrahydromethanopterin
5,10-Methylene-THF
  • (6R)-5,10-methylenetetrahydrofolate
  • 5,10-Methenyltetrahydropteroylglutamate
  • 5,10-Methylene-6-Hydrofolate
  • 5,10-Methylene-6-Hydrofolic acid
  • 5,10-Methylene-THF
31690-11-6
5,6,7,8-Tetrahydromethanopterin
Water
  • Dihydrogen oxide
  • Steam
7732-18-5
genes like me logo Genes that share compounds with SHMT2: view

Transcripts for SHMT2 Gene

Unigene Clusters for SHMT2 Gene

Serine hydroxymethyltransferase 2 (mitochondrial):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SHMT2 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2a · 2b · 2c · 2d · 2e · 2f · 2g · 2h ^ 3a · 3b ^ 4a · 4b · 4c · 4d · 4e · 4f ^ 5a · 5b · 5c ·
SP1: - - - - - - - - - - - - - - - - -
SP2: - - - - - - - - - - - - - - - - -
SP3: - - - - - - - - - -
SP4: - - - - - - - - - -
SP5: - - - - - - - - - - - - - - - - - -
SP6: - - - - - - - - - - - - - - - - -
SP7: - - - - - - - - - - - - - - - - -
SP8: - - - - - - - - - - - - - - - - -
SP9: - - - - - - - - - - - - - - - - -
SP10: - - - - - - - - - - - - - - - - -
SP11: - - - - - - - - - - - - - - - - - - -
SP12: - - - - - - - - - - - - - - - - -
SP13: - - - - - - - - - - - - - - - - -
SP14: - - - - - - - - - -
SP15: - - - - -
SP16: -
SP17: - - -
SP18: - - - -
SP19: - - - - - - - - - - - - - - - - -
SP20:
SP21: - - - - - - - - - - -
SP22: - - - - - - - - - - - - - - - - -
SP23:
SP24:
SP25: - - - - - - - - - - - - - - - - -
SP26: - - - - - - - - - - - - - - - - - - -
SP27: - - - - - - - - - - - -
SP28: - - - - - - - - -
SP29: - - - - - - -
SP30: - - - - -
SP31:
SP32: - - - - - - - - - - - - - - - - -
SP33: -
SP34: -
SP35:
SP36:
SP37:
SP38: - -

ExUns: 5d · 5e ^ 6a · 6b ^ 7a · 7b · 7c · 7d ^ 8 ^ 9a · 9b · 9c · 9d · 9e · 9f · 9g ^ 10a · 10b · 10c · 10d ^ 11a · 11b ^ 12a · 12b ^ 13a · 13b ^
SP1: - - -
SP2: - - - -
SP3: - - - - - - - - - - - - - - - - -
SP4: - - -
SP5: - - - - - - -
SP6: - - - - - - - - - -
SP7: - - - -
SP8: - -
SP9: - -
SP10: -
SP11: - - - - - - - - - -
SP12: - - - - - - - -
SP13: - - - - - -
SP14: - - - - -
SP15: - - -
SP16: - -
SP17: - -
SP18: - -
SP19: - - - - - - - - - - - - - - - -
SP20:
SP21: - -
SP22: - - - -
SP23:
SP24:
SP25: - - -
SP26: - - - - - - - - -
SP27: -
SP28: -
SP29: -
SP30: - - - - -
SP31: - -
SP32: - - - -
SP33: -
SP34: - - - -
SP35: - - - - -
SP36: -
SP37:
SP38:

ExUns: 14a · 14b · 14c · 14d · 14e ^ 15 ^ 16a · 16b · 16c ^ 17a · 17b ^ 18a · 18b · 18c ^ 19a · 19b ^ 20a · 20b · 20c
SP1: -
SP2: -
SP3: -
SP4:
SP5:
SP6: -
SP7:
SP8:
SP9:
SP10:
SP11: -
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19: - - - - - - - - - - - - - - -
SP20: - - -
SP21:
SP22:
SP23: - - -
SP24: - - - - -
SP25:
SP26:
SP27:
SP28:
SP29:
SP30:
SP31:
SP32:
SP33:
SP34:
SP35:
SP36:
SP37: -
SP38:

Relevant External Links for SHMT2 Gene

GeneLoc Exon Structure for
SHMT2
ECgene alternative splicing isoforms for
SHMT2

Expression for SHMT2 Gene

mRNA expression in normal human tissues for SHMT2 Gene

mRNA differential expression in normal tissues according to GTEx for SHMT2 Gene

This gene is overexpressed in Liver (x6.4).

Protein differential expression in normal tissues from HIPED for SHMT2 Gene

This gene is overexpressed in Liver (12.6), Lymph node (8.4), and Peripheral blood mononuclear cells (8.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for SHMT2 Gene



SOURCE GeneReport for Unigene cluster for SHMT2 Gene Hs.741179

genes like me logo Genes that share expression patterns with SHMT2: view

Protein tissue co-expression partners for SHMT2 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt for SHMT2 Gene

Orthologs for SHMT2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SHMT2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SHMT2 36
  • 99 (a)
OneToOne
SHMT2 35
  • 99.28 (n)
  • 98.92 (a)
cow
(Bos Taurus)
Mammalia SHMT2 36
  • 94 (a)
OneToOne
SHMT2 35
  • 90.34 (n)
  • 93.85 (a)
dog
(Canis familiaris)
Mammalia SHMT2 35
  • 91.52 (n)
  • 95.43 (a)
SHMT2 36
  • 87 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Shmt2 36
  • 94 (a)
OneToOne
Shmt2 16
Shmt2 35
  • 87.87 (n)
  • 94.04 (a)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 79 (a)
ManyToMany
rat
(Rattus norvegicus)
Mammalia Shmt2 35
  • 88.4 (n)
  • 94.04 (a)
lizard
(Anolis carolinensis)
Reptilia SHMT2 36
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia shmt2 35
  • 72.59 (n)
  • 81.62 (a)
Str.6934 35
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.849 35
zebrafish
(Danio rerio)
Actinopterygii shmt2 36
  • 78 (a)
OneToOne
shmt2 35
  • 71.75 (n)
  • 78.05 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG3011 36
  • 53 (a)
OneToMany
CG3011 37
  • 60 (a)
worm
(Caenorhabditis elegans)
Secernentea mel-32 37
  • 57 (a)
mel-32 36
  • 54 (a)
OneToMany
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AEL188W 35
  • 55.2 (n)
  • 55.06 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SHM1 35
  • 53.84 (n)
  • 55.26 (a)
SHM1 36
  • 51 (a)
ManyToMany
SHM2 36
  • 54 (a)
ManyToMany
SHM1 38
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F01210g 35
  • 54.32 (n)
  • 53.14 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons SHM1 35
  • 59.99 (n)
  • 62.56 (a)
barley
(Hordeum vulgare)
Liliopsida Hv.3767 35
rice
(Oryza sativa)
Liliopsida Os.12148 35
Os03g0738400 35
  • 59.81 (n)
  • 61.32 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU05805 35
  • 59.45 (n)
  • 58.87 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes shm2 35
  • 55.63 (n)
  • 59.26 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8216 36
  • 65 (a)
OneToOne
Species with no ortholog for SHMT2:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SHMT2 Gene

ENSEMBL:
Gene Tree for SHMT2 (if available)
TreeFam:
Gene Tree for SHMT2 (if available)

Paralogs for SHMT2 Gene

Paralogs for SHMT2 Gene

genes like me logo Genes that share paralogs with SHMT2: view

Variants for SHMT2 Gene

Sequence variations from dbSNP and Humsavar for SHMT2 Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs14201 -- 57,234,310(+) CAACG(A/G/T)GTGGA nc-transcript-variant, reference, synonymous-codon
rs7301155 -- 57,229,038(+) CAAGA(A/G)GTGGA upstream-variant-2KB
rs11615783 -- 57,228,709(+) aaaaa(A/T)ttttt upstream-variant-2KB
rs11557162 -- 57,231,738(+) TGGTG(G/T)ATGAA nc-transcript-variant, reference, missense
rs11557163 -- 57,231,494(+) CAGCC(C/G)AGCTG intron-variant, reference, missense, utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for SHMT2 Gene

Variant ID Type Subtype PubMed ID
dgv96n21 CNV Loss 19592680
nsv519293 CNV Loss 19592680
nsv899116 CNV Loss 21882294

Variation tolerance for SHMT2 Gene

Residual Variation Intolerance Score: 34.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.45; 54.86% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SHMT2 Gene

HapMap Linkage Disequilibrium report
SHMT2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SHMT2 Gene

Disorders for SHMT2 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SHMT2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
pyridoxine deficiency
  • vitamin b6 deficiency
neural tube defects
  • spina bifida
- elite association - COSMIC cancer census association via MalaCards
Search SHMT2 in MalaCards View complete list of genes associated with diseases

Relevant External Links for SHMT2

Genetic Association Database (GAD)
SHMT2
Human Genome Epidemiology (HuGE) Navigator
SHMT2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SHMT2
genes like me logo Genes that share disorders with SHMT2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SHMT2 Gene

Publications for SHMT2 Gene

  1. Molecular cloning, characterization, and regulation of the human mitochondrial serine hydroxymethyltransferase gene. (PMID: 8999870) Stover P.J. … Shane B. (J. Biol. Chem. 1997) 2 3 4 67
  2. Effect of vitamin B6 availability on serine hydroxymethyltransferase in MCF-7 cells. (PMID: 17482557) Perry C. … Stover P.J. (Arch. Biochem. Biophys. 2007) 3 25
  3. Serine hydroxymethyltransferase isoforms are differentially inhibited by leucovorin: characterization and comparison of recombinant zebrafish serine hydroxymethyltransferases. (PMID: 17664250) Chang W.N. … Fu T.F. (Drug Metab. Dispos. 2007) 25 26
  4. The glycine decarboxylase complex multienzyme family in Populus. (PMID: 17355947) Rajinikanth M. … Tsai C.J. (J. Exp. Bot. 2007) 25 26
  5. Molecular cloning and biochemical characterization of Leishmania donovani serine hydroxymethyltransferase. (PMID: 17142057) Vatsyayan R. … Roy U. (Protein Expr. Purif. 2007) 25 26

Products for SHMT2 Gene

Sources for SHMT2 Gene

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