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

    Gene ID: 287379, updated on 2-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 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

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