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    SHM4 serine hydroxymethyltransferase 4 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 827027, updated on 27-Sep-2019

    Summary

    Gene symbol
    SHM4
    Gene description
    serine hydroxymethyltransferase 4
    Primary source
    Araport:AT4G13930
    Locus tag
    AT4G13930
    Gene type
    protein coding
    RNA name
    serine hydroxymethyltransferase 4
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    DL3005C; FCAALL.160; serine hydroxymethyltransferase 4; SERINE HYDROXYMETHYLTRANSFERASE 4
    Summary
    Encodes a serine hydroxymethyltransferase maximally expressed in root

    Genomic context

    See SHM4 in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    4
    Sequence:
    Chromosome: 4; NC_003075.7 (8047692..8050157, complement)

    Chromosome 4 - NC_003075.7Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene receptor like protein 50 Neighboring gene S-adenosyl-L-homocysteine hydrolase Neighboring gene ralf-like 31

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    NM_117467.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    amino acid binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cobalt ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    glycine hydroxymethyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    pyridoxal phosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    serine binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    zinc ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Process Evidence Code Pubs
    L-serine catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cellular response to tetrahydrofolate IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    circadian rhythm IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    folic acid metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    glycine biosynthetic process from serine IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    glycine metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    one-carbon metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    response to cadmium ion IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    tetrahydrofolate interconversion IEA
    Inferred from Electronic Annotation
    more info
     
    tetrahydrofolate metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Component Evidence Code Pubs
    cytoplasm ISM
    Inferred from Sequence Model
    more info
     
    cytosol HDA PubMed 
    cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    plasmodesma IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    serine hydroxymethyltransferase 4
    NP_193129.1
    • serine hydroxymethyltransferase 4 (SHM4); FUNCTIONS IN: pyridoxal phosphate binding, glycine hydroxymethyltransferase activity, catalytic activity; INVOLVED IN: response to cadmium ion, glycine metabolic process, L-serine metabolic process; LOCATED IN: cytosol, plasma membrane, membrane; EXPRESSED IN: 9 plant structures; EXPRESSED DURING: seedling growth, seed development stages; CONTAINS InterPro DOMAIN/s: Pyridoxal phosphate-dependent transferase, major domain (InterPro:IPR015424), Serine hydroxymethyltransferase, pyridoxal phosphate binding site (InterPro:IPR019798), Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (InterPro:IPR015421), Serine hydroxymethyltransferase (InterPro:IPR001085); BEST Arabidopsis thaliana protein match is: Pyridoxal phosphate (PLP)-dependent transferases superfamily protein (TAIR:AT4G13890.1); Has 11689 Blast hits to 11661 proteins in 2862 species: Archae - 259; Bacteria - 6437; Metazoa - 341; Fungi - 289; Plants - 375; Viruses - 6; Other Eukaryotes - 3982 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

    Genome Annotation

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

    Reference assembly

    Genomic

    1. NC_003075.7 Reference assembly

      Range
      8047692..8050157 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_117467.4NP_193129.1  serine hydroxymethyltransferase 4 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_193129.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      O23254
      Conserved Domains (2) summary
      PLN03226
      Location:1471
      PLN03226; serine hydroxymethyltransferase; Provisional
      cl18945
      Location:12412
      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 ...
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