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 136 (02 Jun 2021)
Sequence version 1 (01 Nov 1996)
Previous versions | rss
Add a publicationFeedback
Protein

Diaminopimelate decarboxylase

Gene

lysA

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

Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine.

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 <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

Competitively inhibited by the substrate analog azelaic acid in vitro but not in vivo.1 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

  1. KM=588 µM for meso-2,6-diaminoheptanedioate1 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: L-lysine biosynthesis via DAP pathway

    This protein is involved in step 1 of the subpathway that synthesizes L-lysine from DL-2,6-diaminopimelate.UniRule annotation This subpathway is part of the pathway L-lysine biosynthesis via DAP pathway, 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 L-lysine from DL-2,6-diaminopimelate, the pathway L-lysine biosynthesis via DAP pathway 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 sitei217Pyridoxal phosphate1 Publication1
    Binding sitei254Pyridoxal phosphate; via amide nitrogen1 Publication1
    Binding sitei297Substrate1 Publication1
    Binding sitei333Substrate1 Publication1
    Binding sitei337Substrate1 Publication1
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei362Proton donorUniRule annotation1
    Binding sitei363Substrate1 Publication1
    Binding sitei391Pyridoxal phosphate1 Publication1
    Binding sitei391SubstrateUniRule annotation1

    <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 functionDecarboxylase, Lyase
    Biological processAmino-acid biosynthesis, Lysine biosynthesis
    LigandPyridoxal phosphate

    Enzyme and pathway databases

    SABIO-RK: Biochemical Reaction Kinetics Database

    More...
    SABIO-RKi
    Q58497

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

    More...
    UniPathwayi
    UPA00034;UER00027

    <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:
    Diaminopimelate decarboxylaseUniRule annotation (EC:4.1.1.20UniRule annotation1 Publication)
    Short name:
    DAP decarboxylaseUniRule annotation
    Short name:
    DAPDCUniRule annotation
    <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:lysAUniRule annotation
    Ordered Locus Names:MJ1097
    <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 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_00001499411 – 438Diaminopimelate decarboxylaseAdd BLAST438

    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 residuei73N6-(pyridoxal phosphate)lysine1 Publication1

    <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_1097

    <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

    1438
    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
    Q58497

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    Protein Data Bank in Europe - Knowledge Base

    More...
    PDBe-KBi
    Search...

    Miscellaneous databases

    Relative evolutionary importance of amino acids within a protein sequence

    More...
    EvolutionaryTracei
    Q58497

    <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>Regioni294 – 297Pyridoxal phosphate bindingUniRule annotation1 Publication4

    <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 Orn/Lys/Arg decarboxylase class-II family. LysA subfamily.UniRule annotation

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    arCOG02268, Archaea

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    CLU_026444_0_1_2

    InParanoid: Eukaryotic Ortholog Groups

    More...
    InParanoidi
    Q58497

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    VVGYICE

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    Q58497

    Family and domain databases

    Conserved Domains Database

    More...
    CDDi
    cd06828, PLPDE_III_DapDC, 1 hit

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    2.40.37.10, 1 hit
    3.20.20.10, 1 hit

    HAMAP database of protein families

    More...
    HAMAPi
    MF_02120, LysA, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR009006, Ala_racemase/Decarboxylase_C
    IPR002986, DAP_deCOOHase_LysA
    IPR022643, De-COase2_C
    IPR022657, De-COase2_CS
    IPR022644, De-COase2_N
    IPR022653, De-COase2_pyr-phos_BS
    IPR000183, Orn/DAP/Arg_de-COase
    IPR029066, PLP-binding_barrel

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF02784, Orn_Arg_deC_N, 1 hit
    PF00278, Orn_DAP_Arg_deC, 1 hit

    Protein Motif fingerprint database; a protein domain database

    More...
    PRINTSi
    PR01181, DAPDCRBXLASE
    PR01179, ODADCRBXLASE

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF50621, SSF50621, 2 hits
    SSF51419, SSF51419, 1 hit

    TIGRFAMs; a protein family database

    More...
    TIGRFAMsi
    TIGR01048, lysA, 1 hit

    PROSITE; a protein domain and family database

    More...
    PROSITEi
    View protein in PROSITE
    PS00878, ODR_DC_2_1, 1 hit
    PS00879, ODR_DC_2_2, 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.

    Q58497-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MKIMFLGNDT VEIKDGRFFI DGYDAIELAE KFGTPLYVMS EEQIKINYNR
    60 70 80 90 100
    YIEAFKRWEE ETGKEFIVAY AYKANANLAI TRLLAKLGCG ADVVSGGELY
    110 120 130 140 150
    IAKLSNVPSK KIVFNGNCKT KEEIIMGIEA NIRAFNVDSI SELILINETA
    160 170 180 190 200
    KELGETANVA FRINPNVNPK THPKISTGLK KNKFGLDVES GIAMKAIKMA
    210 220 230 240 250
    LEMEYVNVVG VHCHIGSQLT DISPFIEETR KVMDFVVELK EEGIEIEDVN
    260 270 280 290 300
    LGGGLGIPYY KDKQIPTQKD LADAIINTML KYKDKVEMPN LILEPGRSLV
    310 320 330 340 350
    ATAGYLLGKV HHIKETPVTK WVMIDAGMND MMRPAMYEAY HHIINCKVKN
    360 370 380 390 400
    EKEVVSIAGG LCESSDVFGR DRELDKVEVG DVLAIFDVGA YGISMANNYN
    410 420 430
    ARGRPRMVLT SKKGVFLIRE RETYADLIAK DIVPPHLL
    Length:438
    Mass (Da):48,900
    Last modified:November 1, 1996 - 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:iDE031EC50FD57326
    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: AAB99100.1

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    H64436

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    AAB99100; AAB99100; MJ_1097

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    mja:MJ_1097

    <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: AAB99100.1
    PIRiH64436

    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
    1TUFX-ray2.40A/B5-438[»]
    1TWIX-ray2.00A/B/C/D6-438[»]
    SMRiQ58497
    ModBaseiSearch...
    PDBe-KBiSearch...

    Protein-protein interaction databases

    STRINGi243232.MJ_1097

    Genome annotation databases

    EnsemblBacteriaiAAB99100; AAB99100; MJ_1097
    KEGGimja:MJ_1097

    Phylogenomic databases

    eggNOGiarCOG02268, Archaea
    HOGENOMiCLU_026444_0_1_2
    InParanoidiQ58497
    OMAiVVGYICE
    PhylomeDBiQ58497

    Enzyme and pathway databases

    UniPathwayiUPA00034;UER00027
    SABIO-RKiQ58497

    Miscellaneous databases

    EvolutionaryTraceiQ58497

    Family and domain databases

    CDDicd06828, PLPDE_III_DapDC, 1 hit
    Gene3Di2.40.37.10, 1 hit
    3.20.20.10, 1 hit
    HAMAPiMF_02120, LysA, 1 hit
    InterProiView protein in InterPro
    IPR009006, Ala_racemase/Decarboxylase_C
    IPR002986, DAP_deCOOHase_LysA
    IPR022643, De-COase2_C
    IPR022657, De-COase2_CS
    IPR022644, De-COase2_N
    IPR022653, De-COase2_pyr-phos_BS
    IPR000183, Orn/DAP/Arg_de-COase
    IPR029066, PLP-binding_barrel
    PfamiView protein in Pfam
    PF02784, Orn_Arg_deC_N, 1 hit
    PF00278, Orn_DAP_Arg_deC, 1 hit
    PRINTSiPR01181, DAPDCRBXLASE
    PR01179, ODADCRBXLASE
    SUPFAMiSSF50621, SSF50621, 2 hits
    SSF51419, SSF51419, 1 hit
    TIGRFAMsiTIGR01048, lysA, 1 hit
    PROSITEiView protein in PROSITE
    PS00878, ODR_DC_2_1, 1 hit
    PS00879, ODR_DC_2_2, 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 nameiDCDA_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: Q58497
    <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, 1996
    Last modified: June 2, 2021
    This is version 136 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