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Shmt1 serine hydroxymethyltransferase 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 287379, updated on 27-Nov-2024

Summary

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Official Symbol
Shmt1provided by RGD
Official Full Name
serine hydroxymethyltransferase 1provided by RGD
Primary source
RGD:1312011
See related
EnsemblRapid:ENSRNOG00000005275 AllianceGenome:RGD:1312011
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Shmt; mShmt; LRRGT00032
Summary
Enables several functions, including L-allo-threonine aldolase activity; glycine hydroxymethyltransferase activity; and pyridoxal phosphate binding activity. Involved in glycine biosynthetic process from serine. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in mitochondrion and nucleus. Human ortholog(s) of this gene implicated in breast cancer. Orthologous to human SHMT1 (serine hydroxymethyltransferase 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Liver (RPKM 409.4), Kidney (RPKM 384.7) and 8 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Shmt1 in Genome Data Viewer
Location:
10q22
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (45968959..45990341, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (45468698..45490833, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (47030813..47059216, complement)

Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene DNA topoisomerase III alpha Neighboring gene SMCR8-C9orf72 complex subunit Neighboring gene basic transcription factor 3, pseudogene 15 Neighboring gene dehydrogenase/reductase 7B Neighboring gene small nucleolar RNA SNORA48

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Carnitine biosynthesis. beta-Hydroxylation of trimethyllysine by an alpha-ketoglutarate-dependent mitochondrial dioxygenase. Hulse JD, et al. J Biol Chem, 1978 Mar 10. PMID 627563
  2. Distinct biochemical properties of human serine hydroxymethyltransferase compared with the Plasmodium enzyme: implications for selective inhibition. Pinthong C, et al. FEBS J, 2014 Jun. PMID 24698160
  3. The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy. Renwick SB, et al. Structure, 1998 Sep 15. PMID 9753690
  4. Human cytoplasmic serine hydroxymethyltransferase is an mRNA binding protein. Liu X, et al. Biochemistry, 2000 Sep 26. PMID 10995219
  5. Heavy chain ferritin enhances serine hydroxymethyltransferase expression and de novo thymidine biosynthesis. Oppenheim EW, et al. J Biol Chem, 2001 Jun 8. PMID 11278996

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Identification of AGXT2, SHMT1, and ACO2 as important biomarkers of acute kidney injury by WGCNA.
    Title: Identification of AGXT2, SHMT1, and ACO2 as important biomarkers of acute kidney injury by WGCNA.
  2. The low activity of SHMT in the human and rat placenta suggests that, unlike in the sheep, placental conversion of serine to glycine is not a major source of fetal glycine in these species.
    Title: Low serine hydroxymethyltransferase activity in the human placenta has important implications for fetal glycine supply.
  3. Vitamin B 6 intake affects level of serine hydroxymethyltransferase in rat liver cytosol and mitochondria.
    Title: Activities of hepatic cytosolic and mitochondrial forms of serine hydroxymethyltransferase and hepatic glycine concentration are affected by vitamin B-6 intake in rats.
  4. SHMT enzymes are the major source of the one-carbon unit required for folate metabolism and for the biosynthesis of nucleotides and amino acids. Our data establish a novel functional link between Myc and the regulation of cellular metabolism.
    Title: A functional screen for Myc-responsive genes reveals serine hydroxymethyltransferase, a major source of the one-carbon unit for cell metabolism.
Submit: New GeneRIF Correction

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 RGD

Function Evidence Code Pubs
enables L-allo-threonine aldolase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables aldehyde-lyase activity ISO
Inferred from Sequence Orthology
more info
  
enables amino acid binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables glycine hydroxymethyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables glycine hydroxymethyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables glycine hydroxymethyltransferase activity ISO
Inferred from Sequence Orthology
more info
  
enables glycine hydroxymethyltransferase activity TAS
Traceable Author Statement
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
  
enables mRNA 5'-UTR binding ISO
Inferred from Sequence Orthology
more info
  
enables mRNA regulatory element binding translation repressor activity ISO
Inferred from Sequence Orthology
more info
  
enables protein homodimerization activity ISO
Inferred from Sequence Orthology
more info
  
enables pyridoxal phosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables pyridoxal phosphate binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables pyridoxal phosphate binding ISO
Inferred from Sequence Orthology
more info
  
enables pyridoxal phosphate binding TAS
Traceable Author Statement
more info
 PubMed 
enables serine binding ISO
Inferred from Sequence Orthology
more info
  
enables small molecule binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in L-serine catabolic process ISO
Inferred from Sequence Orthology
more info
  
involved_in L-serine metabolic process ISO
Inferred from Sequence Orthology
more info
  
involved_in L-serine metabolic process TAS
Traceable Author Statement
more info
 PubMed 
acts_upstream_of_or_within cellular response to leukemia inhibitory factor ISO
Inferred from Sequence Orthology
more info
  
involved_in cellular response to tetrahydrofolate ISO
Inferred from Sequence Orthology
more info
  
involved_in dTMP biosynthetic process ISO
Inferred from Sequence Orthology
more info
  
involved_in folic acid metabolic process ISO
Inferred from Sequence Orthology
more info
  
involved_in glycine biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in glycine biosynthetic process from serine IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in glycine biosynthetic process from serine IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in glycine metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in glycine metabolic process ISO
Inferred from Sequence Orthology
more info
  
involved_in glycine metabolic process TAS
Traceable Author Statement
more info
 PubMed 
involved_in negative regulation of translation ISO
Inferred from Sequence Orthology
more info
  
involved_in protein homotetramerization ISO
Inferred from Sequence Orthology
more info
  
involved_in purine nucleobase biosynthetic process ISO
Inferred from Sequence Orthology
more info
  
involved_in tetrahydrofolate interconversion IEA
Inferred from Electronic Annotation
more info
  
involved_in tetrahydrofolate interconversion ISO
Inferred from Sequence Orthology
more info
  
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
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
serine hydroxymethyltransferase, cytosolic
Names
serine hydroxymethyltransferase 1 (soluble)
NP_001400080.1
XP_038941332.1

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_001413151.1 → NP_001400080.1  serine hydroxymethyltransferase, cytosolic

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000010
    UniProtKB/TrEMBL
    A0A8I5ZKU9
    Related
    ENSRNOP00000105844.1, ENSRNOT00000156060.1

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086028.1 Reference GRCr8

    Range
    45968959..45990341 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039085404.2 → XP_038941332.1  serine hydroxymethyltransferase, cytosolic isoform X1

    UniProtKB/TrEMBL
    A6HF57, Q4KLG7
    Conserved Domains (1) summary
    cl18945
    Location:1 → 343
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001047842.1: Suppressed sequence

    Description
    NM_001047842.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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