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Shmt2 serine hydroxymethyltransferase 2 (mitochondrial) [ Mus musculus (house mouse) ]

Gene ID: 108037, updated on 23-Mar-2024

Summary

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Official Symbol
Shmt2provided by MGI
Official Full Name
serine hydroxymethyltransferase 2 (mitochondrial)provided by MGI
Primary source
MGI:MGI:1277989
See related
Ensembl:ENSMUSG00000025403 AllianceGenome:MGI:1277989
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
SHMT; 2700043D08Rik
Summary
Enables glycine hydroxymethyltransferase activity. Involved in regulation of mitochondrial translation; regulation of oxidative phosphorylation; and tetrahydrofolate interconversion. Located in nucleus. Is expressed in several structures, including brain; neural retina; placenta; skeleton; and submandibular gland primordium. Orthologous to human SHMT2 (serine hydroxymethyltransferase 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in liver adult (RPKM 102.9), kidney adult (RPKM 81.2) and 27 other tissues See more
Orthologs
human all
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Genomic context

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Location:
10 D3; 10 74.51 cM
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (127352992..127358313, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (127517123..127522444, complement)

Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene R3H domain containing 2 Neighboring gene predicted gene, 23819 Neighboring gene STARR-positive B cell enhancer mm9_chr10:126945421-126945721 Neighboring gene STARR-positive B cell enhancer ABC_E10656 Neighboring gene STARR-positive B cell enhancer ABC_E2342 Neighboring gene Ndufa4, mitochondrial complex associated like 2 Neighboring gene STARR-positive B cell enhancer ABC_E1132 Neighboring gene SH3 and cysteine rich domain 3 Neighboring gene neurexophilin 4 Neighboring gene low density lipoprotein receptor-related protein 1 Neighboring gene STARR-seq mESC enhancer starr_28231 Neighboring gene predicted gene 16217

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. The role of SHMT2 in modulating lipid metabolism in hepatocytes via glycine-mediated mTOR activation. Choi YJ, et al. Amino Acids, 2022 May. PMID 35212811
  2. Disruption of the mouse Shmt2 gene confers embryonic anaemia via foetal liver-specific metabolomic disorders. Tani H, et al. Sci Rep, 2019 Nov 5. PMID 31690790, Free PMC Article
  3. SHMT2 Promotes Liver Regeneration Through Glycine-activated Akt/mTOR Pathway. Wang M, et al. Transplantation, 2019 Jul. PMID 30964837
  4. Downregulating Serine Hydroxymethyltransferase 2 Deteriorates Hepatic Ischemia-Reperfusion Injury through ROS/JNK/P53 Signaling in Mice. Wu H, et al. Biomed Res Int, 2019. PMID 31828098, Free PMC Article
  5. Loss of PYCR2 Causes Neurodegeneration by Increasing Cerebral Glycine Levels via SHMT2. Escande-Beillard N, et al. Neuron, 2020 Jul 8. PMID 32330411

See all (38) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SHMT2 Mediates Small-Molecule-Induced Alleviation of Alzheimer Pathology Via the 5'UTR-dependent ADAM10 Translation Initiation.
    Title: SHMT2 Mediates Small-Molecule-Induced Alleviation of Alzheimer Pathology Via the 5'UTR-dependent ADAM10 Translation Initiation.
  2. SHMT2 reduces fatty liver but is necessary for liver inflammation and fibrosis in mice.
    Title: SHMT2 reduces fatty liver but is necessary for liver inflammation and fibrosis in mice.
  3. Serine synthesis via reversed SHMT2 activity drives glycine depletion and acetaminophen hepatotoxicity in MASLD.
    Title: Serine synthesis via reversed SHMT2 activity drives glycine depletion and acetaminophen hepatotoxicity in MASLD.
  4. The role of SHMT2 in modulating lipid metabolism in hepatocytes via glycine-mediated mTOR activation.
    Title: The role of SHMT2 in modulating lipid metabolism in hepatocytes via glycine-mediated mTOR activation.
  5. Disruption of the mouse Shmt2 gene confers embryonic anaemia via foetal liver-specific metabolomic disorders.
    Title: Disruption of the mouse Shmt2 gene confers embryonic anaemia via foetal liver-specific metabolomic disorders.
  6. Loss of PYCR2 Causes Neurodegeneration by Increasing Cerebral Glycine Levels via SHMT2.
    Title: Loss of PYCR2 Causes Neurodegeneration by Increasing Cerebral Glycine Levels via SHMT2.
  7. SHMT2 can contribute to liver regeneration after partial hepatectomy, and this is likely related to the activation of Akt/mTOR signaling pathway by its metabolic product, glycine, in hepatocytes.
    Title: SHMT2 Promotes Liver Regeneration Through Glycine-activated Akt/mTOR Pathway.
  8. Knockdown of SHMT2 worsens IR injury through the ROS/JNK/P53 signaling pathway.
    Title: Downregulating Serine Hydroxymethyltransferase 2 Deteriorates Hepatic Ischemia-Reperfusion Injury through ROS/JNK/P53 Signaling in Mice.
  9. SHMT1 and SHMT2 are functionally redundant in nuclear de novo thymidylate biosynthesis
    Title: SHMT1 and SHMT2 are functionally redundant in nuclear de novo thymidylate biosynthesis.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Gene trapped (1) 
  • Endonuclease-mediated (6)  1 citation

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables L-allo-threonine aldolase activity ISO
Inferred from Sequence Orthology
more info
  
enables amino acid binding ISO
Inferred from Sequence Orthology
more info
  
enables chromatin binding ISO
Inferred from Sequence Orthology
more info
  
enables glycine hydroxymethyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables glycine hydroxymethyltransferase activity IGI
Inferred from Genetic Interaction
more info
 PubMed 
enables glycine hydroxymethyltransferase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables glycine hydroxymethyltransferase activity ISO
Inferred from Sequence Orthology
more info
  
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
  
enables pyridoxal phosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables pyridoxal phosphate binding ISO
Inferred from Sequence Orthology
more info
  
enables transferase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in L-serine biosynthetic process ISO
Inferred from Sequence Orthology
more info
  
involved_in L-serine metabolic process ISO
Inferred from Sequence Orthology
more info
  
involved_in glycine biosynthetic process ISO
Inferred from Sequence Orthology
more info
  
involved_in glycine biosynthetic process from serine IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in glycine biosynthetic process from serine ISO
Inferred from Sequence Orthology
more info
  
involved_in glycine metabolic process ISO
Inferred from Sequence Orthology
more info
  
involved_in one-carbon metabolic process ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of cell population proliferation ISO
Inferred from Sequence Orthology
more info
  
involved_in protein K63-linked deubiquitination ISO
Inferred from Sequence Orthology
more info
  
involved_in protein homotetramerization ISO
Inferred from Sequence Orthology
more info
  
involved_in protein tetramerization ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of aerobic respiration IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of aerobic respiration ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of mitochondrial translation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of mitochondrial translation ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of oxidative phosphorylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of oxidative phosphorylation ISO
Inferred from Sequence Orthology
more info
  
involved_in response to type I interferon ISO
Inferred from Sequence Orthology
more info
  
involved_in tetrahydrofolate interconversion IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in tetrahydrofolate metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in tetrahydrofolate metabolic process ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
part_of BRISC complex ISO
Inferred from Sequence Orthology
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in microtubule cytoskeleton ISO
Inferred from Sequence Orthology
more info
  
located_in mitochondrial inner membrane HDA PubMed 
located_in mitochondrial inner membrane ISO
Inferred from Sequence Orthology
more info
  
located_in mitochondrial matrix ISO
Inferred from Sequence Orthology
more info
  
located_in mitochondrial nucleoid ISO
Inferred from Sequence Orthology
more info
  
located_in mitochondrion HDA PubMed 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrion ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleus IGI
Inferred from Genetic Interaction
more info
 PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
serine hydroxymethyltransferase, mitochondrial
Names
glycine hydroxymethyltransferase
serine methylase
NP_001239245.1
NP_082506.1

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

  1. NM_001252316.1 → NP_001239245.1  serine hydroxymethyltransferase, mitochondrial isoform 2

    See identical proteins and their annotated locations for NP_001239245.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses a different splice site in the 5' coding region, compared to variant 1. The resulting protein (isoform 2) has a shorter N-terminus when it is compared to isoform 1.
    Source sequence(s)
    AK162421, AK169192
    Consensus CDS
    CCDS88105.1
    UniProtKB/TrEMBL
    Q3TFD0, Q9CZN7
    Related
    ENSMUSP00000151616.2, ENSMUST00000219239.2
    Conserved Domains (1) summary
    PLN03226
    Location:42 → 499
    PLN03226; serine hydroxymethyltransferase; Provisional

  2. NM_028230.4 → NP_082506.1  serine hydroxymethyltransferase, mitochondrial isoform 1

    See identical proteins and their annotated locations for NP_082506.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and it encodes the longer protein (isoform 1).
    Source sequence(s)
    AK162421, BY760884
    Consensus CDS
    CCDS24244.1
    UniProtKB/Swiss-Prot
    Q3TFD0, Q99K87, Q9CZN7
    Related
    ENSMUSP00000026470.5, ENSMUST00000026470.6
    Conserved Domains (1) summary
    PLN03226
    Location:45 → 502
    PLN03226; serine hydroxymethyltransferase; Provisional

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000076.7 Reference GRCm39 C57BL/6J

    Range
    127352992..127358313 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9CZN7.1 GenPept UniProtKB/Swiss-Prot:Q9CZN7

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