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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-Experimental evidence at protein leveli

Functioni

Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine.1 Publication

Catalytic activityi

Meso-2,6-diaminoheptanedioate = L-lysine + CO2.1 Publication

Cofactori

pyridoxal 5'-phosphate1 Publication

Enzyme regulationi

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

Kineticsi

  1. KM=588 µM for meso-2,6-diaminoheptanedioate1 Publication

    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
    Proteins known to be involved in this subpathway in this organism are:
    1. Diaminopimelate decarboxylase (lysA)
    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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei217 – 2171Pyridoxal phosphate1 Publication
    Binding sitei254 – 2541Pyridoxal phosphate; via amide nitrogen1 Publication
    Binding sitei297 – 2971Substrate1 Publication
    Binding sitei333 – 3331Substrate1 Publication
    Binding sitei337 – 3371Substrate1 Publication
    Active sitei362 – 3621Proton donorUniRule annotation
    Binding sitei363 – 3631Substrate1 Publication
    Binding sitei391 – 3911Pyridoxal phosphate1 Publication
    Binding sitei391 – 3911SubstrateUniRule annotation

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Decarboxylase, Lyase

    Keywords - Biological processi

    Amino-acid biosynthesis, Lysine biosynthesis

    Keywords - Ligandi

    Pyridoxal phosphate

    Enzyme and pathway databases

    UniPathwayiUPA00034; UER00027.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Diaminopimelate decarboxylaseUniRule annotation (EC:4.1.1.20UniRule annotation1 Publication)
    Short name:
    DAP decarboxylaseUniRule annotation
    Short name:
    DAPDCUniRule annotation
    Gene namesi
    Name:lysAUniRule annotation
    Ordered Locus Names:MJ1097
    OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
    Taxonomic identifieri243232 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
    Proteomesi
    • UP000000805 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 438438Diaminopimelate decarboxylasePRO_0000149941Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei73 – 731N6-(pyridoxal phosphate)lysine1 Publication

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    STRINGi243232.MJ_1097.

    Structurei

    Secondary structure

    1
    438
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi11 – 144Combined sources
    Beta strandi17 – 204Combined sources
    Helixi25 – 328Combined sources
    Beta strandi34 – 407Combined sources
    Helixi41 – 6222Combined sources
    Beta strandi66 – 716Combined sources
    Helixi72 – 743Combined sources
    Helixi78 – 869Combined sources
    Beta strandi90 – 934Combined sources
    Helixi96 – 1049Combined sources
    Helixi109 – 1113Combined sources
    Beta strandi112 – 1143Combined sources
    Helixi121 – 1299Combined sources
    Beta strandi133 – 1375Combined sources
    Helixi140 – 15314Combined sources
    Beta strandi157 – 1648Combined sources
    Turni169 – 1713Combined sources
    Helixi173 – 1819Combined sources
    Beta strandi185 – 1884Combined sources
    Helixi192 – 20211Combined sources
    Beta strandi204 – 2129Combined sources
    Beta strandi217 – 2193Combined sources
    Helixi223 – 24119Combined sources
    Beta strandi247 – 2504Combined sources
    Beta strandi259 – 2635Combined sources
    Helixi268 – 28013Combined sources
    Turni281 – 2855Combined sources
    Beta strandi290 – 2934Combined sources
    Helixi297 – 3004Combined sources
    Helixi301 – 3033Combined sources
    Beta strandi304 – 31512Combined sources
    Beta strandi320 – 3256Combined sources
    Turni328 – 3303Combined sources
    Helixi333 – 3375Combined sources
    Beta strandi343 – 3475Combined sources
    Beta strandi352 – 3587Combined sources
    Beta strandi360 – 3623Combined sources
    Beta strandi367 – 3759Combined sources
    Beta strandi382 – 3865Combined sources
    Beta strandi389 – 3924Combined sources
    Helixi393 – 3953Combined sources
    Turni399 – 4013Combined sources
    Beta strandi406 – 4116Combined sources
    Beta strandi414 – 4196Combined sources
    Helixi424 – 4274Combined sources
    Turni428 – 4303Combined sources
    Helixi435 – 4373Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1TUFX-ray2.40A/B5-438[»]
    1TWIX-ray2.00A/B/C/D6-438[»]
    ProteinModelPortaliQ58497.
    SMRiQ58497. Positions 6-438.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ58497.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni294 – 2974Pyridoxal phosphate bindingUniRule annotation1 Publication

    Sequence similaritiesi

    Belongs to the Orn/Lys/Arg decarboxylase class-II family. LysA subfamily.UniRule annotation

    Phylogenomic databases

    eggNOGiarCOG02268. Archaea.
    COG0019. LUCA.
    InParanoidiQ58497.
    KOiK01586.
    OMAiLKGNKFG.
    PhylomeDBiQ58497.

    Family and domain databases

    Gene3Di2.40.37.10. 1 hit.
    3.20.20.10. 1 hit.
    HAMAPiMF_02120. LysA. 1 hit.
    InterProiIPR009006. 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.
    [Graphical view]
    PfamiPF02784. Orn_Arg_deC_N. 1 hit.
    PF00278. Orn_DAP_Arg_deC. 1 hit.
    [Graphical view]
    PRINTSiPR01181. DAPDCRBXLASE.
    PR01179. ODADCRBXLASE.
    SUPFAMiSSF50621. SSF50621. 2 hits.
    SSF51419. SSF51419. 1 hit.
    TIGRFAMsiTIGR01048. lysA. 1 hit.
    PROSITEiPS00878. ODR_DC_2_1. 1 hit.
    PS00879. ODR_DC_2_2. 1 hit.
    [Graphical view]

    Sequencei

    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
    Checksum:iDE031EC50FD57326
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L77117 Genomic DNA. Translation: AAB99100.1.
    PIRiH64436.

    Genome annotation databases

    EnsemblBacteriaiAAB99100; AAB99100; MJ_1097.
    KEGGimja:MJ_1097.

    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:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1TUFX-ray2.40A/B5-438[»]
    1TWIX-ray2.00A/B/C/D6-438[»]
    ProteinModelPortaliQ58497.
    SMRiQ58497. Positions 6-438.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi243232.MJ_1097.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAB99100; AAB99100; MJ_1097.
    KEGGimja:MJ_1097.

    Phylogenomic databases

    eggNOGiarCOG02268. Archaea.
    COG0019. LUCA.
    InParanoidiQ58497.
    KOiK01586.
    OMAiLKGNKFG.
    PhylomeDBiQ58497.

    Enzyme and pathway databases

    UniPathwayiUPA00034; UER00027.

    Miscellaneous databases

    EvolutionaryTraceiQ58497.

    Family and domain databases

    Gene3Di2.40.37.10. 1 hit.
    3.20.20.10. 1 hit.
    HAMAPiMF_02120. LysA. 1 hit.
    InterProiIPR009006. 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.
    [Graphical view]
    PfamiPF02784. Orn_Arg_deC_N. 1 hit.
    PF00278. Orn_DAP_Arg_deC. 1 hit.
    [Graphical view]
    PRINTSiPR01181. DAPDCRBXLASE.
    PR01179. ODADCRBXLASE.
    SUPFAMiSSF50621. SSF50621. 2 hits.
    SSF51419. SSF51419. 1 hit.
    TIGRFAMsiTIGR01048. lysA. 1 hit.
    PROSITEiPS00878. ODR_DC_2_1. 1 hit.
    PS00879. ODR_DC_2_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiDCDA_METJA
    AccessioniPrimary (citable) accession number: Q58497
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 1, 1996
    Last modified: February 17, 2016
    This is version 113 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Methanococcus jannaschii
      Methanococcus jannaschii: entries and gene names
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.