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SHMT2 serine hydroxymethyltransferase 2 (mitochondrial) [ Homo sapiens (human) ]

Gene ID: 6472, updated on 6-Jul-2014
Official Symbol
SHMT2provided by HGNC
Official Full Name
serine hydroxymethyltransferase 2 (mitochondrial)provided by HGNC
Primary source
HGNC:10852
See related
Ensembl:ENSG00000182199; HPRD:00717; MIM:138450; Vega:OTTHUMG00000171246
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
GLYA; SHMT; HEL-S-51e
Summary
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]
See SHMT2 in Epigenomics, MapViewer
Location:
12q12-q14
Exon count :
14
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 12 NC_000012.12 (57229573..57234935)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (57623356..57628718)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene low density lipoprotein receptor-related protein 1 Neighboring gene microRNA 1228 Neighboring gene neurexophilin 4 Neighboring gene NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4-like 2 Neighboring gene SH3 and cysteine rich domain 3 Neighboring gene R3H domain containing 2 Neighboring gene uncharacterized LOC102724177

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
L-allo-threonine aldolase activity IEA
Inferred from Electronic Annotation
more info
 
amino acid binding IEA
Inferred from Electronic Annotation
more info
 
chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
glycine hydroxymethyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IEA
Inferred from Electronic Annotation
more info
 
pyridoxal phosphate binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
L-serine biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
glycine biosynthetic process from serine IEA
Inferred from Electronic Annotation
more info
 
one-carbon metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell proliferation IEA
Inferred from Electronic Annotation
more info
 
protein homotetramerization IEA
Inferred from Electronic Annotation
more info
 
tetrahydrofolate interconversion IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
extracellular vesicular exosome IDA
Inferred from Direct Assay
more info
PubMed 
microtubule cytoskeleton IDA
Inferred from Direct Assay
more info
 
mitochondrial inner membrane IDA
Inferred from Direct Assay
more info
 
mitochondrial intermembrane space IEA
Inferred from Electronic Annotation
more info
 
mitochondrial matrix IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrial nucleoid IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrion IDA
Inferred from Direct Assay
more info
 
Preferred Names
serine hydroxymethyltransferase, mitochondrial
Names
serine hydroxymethyltransferase, mitochondrial
GLY A+
serine aldolase
serine methylase
threonine aldolase
serine hydroxymethylase
glycine hydroxymethyltransferase
epididymis secretory sperm binding protein Li 51e
glycine auxotroph A, human complement for hamster
NP_001159828.1
NP_001159829.1
NP_001159830.1
NP_001159831.1
NP_005403.2

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_029163.1 

    Range
    5001..10363
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001166356.1NP_001159828.1  serine hydroxymethyltransferase, mitochondrial isoform 2 precursor

    See proteins identical to NP_001159828.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    BC032584, BC091501, DC386590
    Consensus CDS
    CCDS55837.1
    UniProtKB/Swiss-Prot
    P34897
    UniProtKB/TrEMBL
    Q5BJF5
    Related
    ENSP00000452315, OTTHUMP00000245570, ENST00000557487, OTTHUMT00000412539
    Conserved Domains (1) summary
    cd00378
    Location:51455
    Blast Score: 1552
    SHMT; Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl ...
  2. NM_001166357.1NP_001159829.1  serine hydroxymethyltransferase, mitochondrial isoform 3

    See proteins identical to NP_001159829.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) is the longest transcript. It differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3, 4, and 5 encode the same isoform 3. Translation efficiency is uncertain from this alternative start codon, and there is rapid turnover of the mitochondrial protein in the cytoplasm prior to mitochondrial import due to its shortened import presequence (PMID 8999870).
    Source sequence(s)
    AK315916, BC091501, DC339924
    Consensus CDS
    CCDS53805.1
    UniProtKB/Swiss-Prot
    P34897
    UniProtKB/TrEMBL
    Q5BJF5
    Related
    ENSP00000413770, OTTHUMP00000245566, ENST00000449049, OTTHUMT00000412534
    Conserved Domains (1) summary
    cd00378
    Location:30444
    Blast Score: 1610
    SHMT; Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl ...
  3. NM_001166358.1NP_001159830.1  serine hydroxymethyltransferase, mitochondrial isoform 3

    See proteins identical to NP_001159830.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3, 4, and 5 encode the same isoform 3. Translation efficiency is uncertain from this alternative start codon, and there is rapid turnover of the mitochondrial protein in the cytoplasm prior to mitochondrial import due to its shortened import presequence (PMID 8999870).
    Source sequence(s)
    AC137834, BC091501, BX647711, DA052422
    Consensus CDS
    CCDS53805.1
    UniProtKB/Swiss-Prot
    P34897
    UniProtKB/TrEMBL
    Q5BJF5
    UniProtKB/TrEMBL
    Q5HYG8
    Related
    ENSP00000406881, OTTHUMP00000245562, ENST00000414700, OTTHUMT00000412529
    Conserved Domains (1) summary
    cd00378
    Location:30444
    Blast Score: 1610
    SHMT; Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl ...
  4. NM_001166359.1NP_001159831.1  serine hydroxymethyltransferase, mitochondrial isoform 3

    See proteins identical to NP_001159831.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3, 4, and 5 encode the same isoform 3. Translation efficiency is uncertain from this alternative start codon, and there is rapid turnover of the mitochondrial protein in the cytoplasm prior to mitochondrial import due to its shortened import presequence (PMID 8999870).
    Source sequence(s)
    AC137834, AK296183, BC091501, CN395976
    Consensus CDS
    CCDS53805.1
    UniProtKB/TrEMBL
    B4DJQ3
    UniProtKB/Swiss-Prot
    P34897
    UniProtKB/TrEMBL
    Q5BJF5
    Related
    ENSP00000452419, OTTHUMP00000245565, ENST00000553474, OTTHUMT00000412533
    Conserved Domains (1) summary
    cd00378
    Location:30444
    Blast Score: 1610
    SHMT; Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl ...
  5. NM_005412.5NP_005403.2  serine hydroxymethyltransferase, mitochondrial isoform 1 precursor

    See proteins identical to NP_005403.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    BC011911, BC091501, DC386590
    Consensus CDS
    CCDS8934.1
    UniProtKB/Swiss-Prot
    P34897
    UniProtKB/TrEMBL
    Q5BJF5
    UniProtKB/TrEMBL
    V9HW06
    Related
    ENSP00000333667, OTTHUMP00000245559, ENST00000328923, OTTHUMT00000412525
    Conserved Domains (1) summary
    cd00378
    Location:51465
    Blast Score: 1616
    SHMT; Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl ...

RNA

  1. NR_029415.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) contains an alternate 5' exon and lacks an internal exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region and is likely a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC137834, AK297173, BC091501, CN395976
  2. NR_029416.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) contains an alternate 5' exon and lacks an internal exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region and is likely a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC137834, AK301443, BC091501, DA052422
  3. NR_029417.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BC091501, DC386590
  4. NR_048562.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) contains an alternate 5' exon, lacks an internal exon, and uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BC008711

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000012.12 

    Range
    57229573..57234935
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

  1. AC_000144.1 

    Range
    54662237..54667595
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018923.2 

    Range
    57591454..57596816
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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