Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Entry version 128 (02 Jun 2021)
Sequence version 1 (01 Nov 1997)
Previous versions | rss
Add a publicationFeedback
Protein

Serine hydroxymethyltransferase

Gene

glyA

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Catalyzes the reversible interconversion of serine and glycine with tetrahydromethanopterin (H4MPT) serving as the one-carbon carrier. The use of tetrahydrofolate (THF or H4PteGlu) as the pteridine substrate is 450-fold less efficient than that of H4MPT. Also exhibits a pteridine-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism. Thus, is able to catalyze the cleavage of L-allo-threonine and L-threo-beta-phenylserine.

1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

pyridoxal 5'-phosphate1 Publication

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

kcat is 212 min(-1) for the L-serine hydroxymethyltransferase reaction, and 687 min(-1) for the L-allo-threonine cleavage, at 37 and 60 degrees Celsius, respectively. The presence of oxygen does not seem to affect significantly the kinetic parameters of the reactions.
  1. KM=0.8 mM for L-serine (at 37 degrees Celsius)1 Publication
  2. KM=0.1 mM for tetrahydromethanopterin (at 37 degrees Celsius)1 Publication
  3. KM=1.3 mM for L-allo-threonine (at 60 degrees Celsius)1 Publication
  4. KM=95 mM for DL-threo-beta-phenylserine (at 60 degrees Celsius)1 Publication

    Temperature dependencei

    Optimum temperature is 70-80 degrees Celsius for the retro-aldol cleavage of L-allo-threonine.1 Publication

    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: glycine biosynthesis

    This protein is involved in step 1 of the subpathway that synthesizes glycine from L-serine. This subpathway is part of the pathway glycine biosynthesis, which is itself part of Amino-acid biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes glycine from L-serine, the pathway glycine biosynthesis and in Amino-acid biosynthesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei30Pyridoxal phosphateBy similarity1
    Binding sitei50Pyridoxal phosphateBy similarity1
    Binding sitei52SubstrateBy similarity1
    Binding sitei60Pyridoxal phosphateBy similarity1
    Binding sitei171Pyridoxal phosphateBy similarity1
    Binding sitei199Pyridoxal phosphateBy similarity1
    Binding sitei225Pyridoxal phosphateBy similarity1
    Binding sitei363Pyridoxal phosphateBy similarity1

    <p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

    GO - Biological processi

    <p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

    Molecular functionLyase, Transferase
    Biological processAmino-acid biosynthesis, One-carbon metabolism
    LigandPyridoxal phosphate

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    MJAN243232:G1GKE-1725-MONOMER

    BRENDA Comprehensive Enzyme Information System

    More...
    BRENDAi
    2.1.2.1, 3260

    UniPathway: a resource for the exploration and annotation of metabolic pathways

    More...
    UniPathwayi
    UPA00288;UER01023

    <p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
    Recommended name:
    Serine hydroxymethyltransferase (EC:2.1.2.-)
    Short name:
    SHMT
    Short name:
    Serine methylase
    Alternative name(s):
    L-allo-threonine aldolase (EC:4.1.2.49)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
    Name:glyA
    Ordered Locus Names:MJ1597
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri243232 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiArchaeaEuryarchaeotaMethanomada groupMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
    • UP000000805 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

    <p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

    Keywords - Cellular componenti

    Cytoplasm

    <p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001137131 – 429Serine hydroxymethyltransferaseAdd BLAST429

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'PTM / Processing' section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei226N6-(pyridoxal phosphate)lysineBy similarity1

    <p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

    <p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

    Homodimer.

    1 Publication

    Protein-protein interaction databases

    STRING: functional protein association networks

    More...
    STRINGi
    243232.MJ_1597

    <p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

    Secondary structure

    1429
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    SWISS-MODEL Repository - a database of annotated 3D protein structure models

    More...
    SMRi
    Q58992

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    Protein Data Bank in Europe - Knowledge Base

    More...
    PDBe-KBi
    Search...

    <p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni120 – 122Substrate bindingBy similarity3

    <p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

    Belongs to the SHMT family.Curated

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    arCOG00070, Archaea

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    CLU_022477_2_1_2

    InParanoid: Eukaryotic Ortholog Groups

    More...
    InParanoidi
    Q58992

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    PLEHIIA

    Database of Orthologous Groups

    More...
    OrthoDBi
    22518at2157

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    Q58992

    Family and domain databases

    Conserved Domains Database

    More...
    CDDi
    cd00378, SHMT, 1 hit

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    3.40.640.10, 1 hit
    3.90.1150.10, 1 hit

    HAMAP database of protein families

    More...
    HAMAPi
    MF_00051, SHMT, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR015424, PyrdxlP-dep_Trfase
    IPR015422, PyrdxlP-dep_Trfase_dom1
    IPR015421, PyrdxlP-dep_Trfase_major
    IPR001085, Ser_HO-MeTrfase
    IPR019798, Ser_HO-MeTrfase_PLP_BS
    IPR039429, SHMT-like_dom

    The PANTHER Classification System

    More...
    PANTHERi
    PTHR11680, PTHR11680, 1 hit

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF00464, SHMT, 1 hit

    PIRSF; a whole-protein classification database

    More...
    PIRSFi
    PIRSF000412, SHMT, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF53383, SSF53383, 1 hit

    PROSITE; a protein domain and family database

    More...
    PROSITEi
    View protein in PROSITE
    PS00096, SHMT, 1 hit

    <p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

    Q58992-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MEYSDVPKFI RDVSIKQHEW MRESIKLIAS ENITSLAVRE ACATDFMHRY
    60 70 80 90 100
    AEGLPGKRLY QGCKYIDEVE TLCIELSKEL FKAEHANVQP TSGVVANLAV
    110 120 130 140 150
    FFAETKPGDK LMALSVPDGG HISHWKVSAA GIRGLKVINH PFDPEEMNID
    160 170 180 190 200
    ADAMVKKILE EKPKLILFGG SLFPFPHPVA DAYEAAQEVG AKIAYDGAHV
    210 220 230 240 250
    LGLIAGKQFQ DPLREGAEYL MGSTHKTFFG PQGGVILTTK ENADKIDSHV
    260 270 280 290 300
    FPGVVSNHHL HHKAGLAIAL AEMLEFGEAY AKQVIKNAKA LAQALYERGF
    310 320 330 340 350
    NVLCEHKDFT ESHQVIIDIE SSPDIEFSAS ELAKMYEEAN IILNKNLLPW
    360 370 380 390 400
    DDVNNSDNPS GIRLGTQECT RLGMKEKEME EIAEFMKRIA IDKEKPEKVR
    410 420
    EDVKEFAKEY STIHYSFDEG DGFKYLRFY
    Length:429
    Mass (Da):48,084
    Last modified:November 1, 1997 - v1
    <p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iC115CECA4E649C7A
    GO

    Sequence databases

    Select the link destinations:

    EMBL nucleotide sequence database

    More...
    EMBLi

    GenBank nucleotide sequence database

    More...
    GenBanki

    DNA Data Bank of Japan; a nucleotide sequence database

    More...
    DDBJi
    Links Updated
    L77117 Genomic DNA Translation: AAB99615.1

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    D64499

    NCBI Reference Sequences

    More...
    RefSeqi
    WP_010871121.1, NC_000909.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    AAB99615; AAB99615; MJ_1597

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    1452505

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    mja:MJ_1597

    <p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

    <p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L77117 Genomic DNA Translation: AAB99615.1
    PIRiD64499
    RefSeqiWP_010871121.1, NC_000909.1

    3D structure databases

    Select the link destinations:

    Protein Data Bank Europe

    More...
    PDBei

    Protein Data Bank RCSB

    More...
    RCSB PDBi

    Protein Data Bank Japan

    More...
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4BHDX-ray2.83A/B3-429[»]
    4UQVX-ray3.00A/B/C/D/E/F/G/H/I/J/K/L1-429[»]
    SMRiQ58992
    ModBaseiSearch...
    PDBe-KBiSearch...

    Protein-protein interaction databases

    STRINGi243232.MJ_1597

    Genome annotation databases

    EnsemblBacteriaiAAB99615; AAB99615; MJ_1597
    GeneIDi1452505
    KEGGimja:MJ_1597

    Phylogenomic databases

    eggNOGiarCOG00070, Archaea
    HOGENOMiCLU_022477_2_1_2
    InParanoidiQ58992
    OMAiPLEHIIA
    OrthoDBi22518at2157
    PhylomeDBiQ58992

    Enzyme and pathway databases

    UniPathwayiUPA00288;UER01023
    BioCyciMJAN243232:G1GKE-1725-MONOMER
    BRENDAi2.1.2.1, 3260

    Family and domain databases

    CDDicd00378, SHMT, 1 hit
    Gene3Di3.40.640.10, 1 hit
    3.90.1150.10, 1 hit
    HAMAPiMF_00051, SHMT, 1 hit
    InterProiView protein in InterPro
    IPR015424, PyrdxlP-dep_Trfase
    IPR015422, PyrdxlP-dep_Trfase_dom1
    IPR015421, PyrdxlP-dep_Trfase_major
    IPR001085, Ser_HO-MeTrfase
    IPR019798, Ser_HO-MeTrfase_PLP_BS
    IPR039429, SHMT-like_dom
    PANTHERiPTHR11680, PTHR11680, 1 hit
    PfamiView protein in Pfam
    PF00464, SHMT, 1 hit
    PIRSFiPIRSF000412, SHMT, 1 hit
    SUPFAMiSSF53383, SSF53383, 1 hit
    PROSITEiView protein in PROSITE
    PS00096, SHMT, 1 hit

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    Search...

    <p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

    <p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiGLYA_METJA
    <p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q58992
    <p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 1, 1997
    Last modified: June 2, 2021
    This is version 128 of the entry and version 1 of the sequence. See complete history.
    <p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    <p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

    Keywords - Technical termi

    3D-structure, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families
    UniProt is an ELIXIR core data resource
    Main funding by: National Institutes of Health

    We'd like to inform you that we have updated our Privacy Notice to comply with Europe’s new General Data Protection Regulation (GDPR) that applies since 25 May 2018.

    Do not show this banner again