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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)DescriptionActionsGraphical viewLength
    Binding sitei217Pyridoxal phosphate1 Publication1
    Binding sitei254Pyridoxal phosphate; via amide nitrogen1 Publication1
    Binding sitei297Substrate1 Publication1
    Binding sitei333Substrate1 Publication1
    Binding sitei337Substrate1 Publication1
    Active sitei362Proton donorUniRule annotation1
    Binding sitei363Substrate1 Publication1
    Binding sitei391Pyridoxal phosphate1 Publication1
    Binding sitei391SubstrateUniRule annotation1

    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)DescriptionActionsGraphical viewLength
    ChainiPRO_00001499411 – 438Diaminopimelate decarboxylaseAdd BLAST438

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei73N6-(pyridoxal phosphate)lysine1 Publication1

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    STRINGi243232.MJ_1097.

    Structurei

    Secondary structure

    1438
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi11 – 14Combined sources4
    Beta strandi17 – 20Combined sources4
    Helixi25 – 32Combined sources8
    Beta strandi34 – 40Combined sources7
    Helixi41 – 62Combined sources22
    Beta strandi66 – 71Combined sources6
    Helixi72 – 74Combined sources3
    Helixi78 – 86Combined sources9
    Beta strandi90 – 93Combined sources4
    Helixi96 – 104Combined sources9
    Helixi109 – 111Combined sources3
    Beta strandi112 – 114Combined sources3
    Helixi121 – 129Combined sources9
    Beta strandi133 – 137Combined sources5
    Helixi140 – 153Combined sources14
    Beta strandi157 – 164Combined sources8
    Turni169 – 171Combined sources3
    Helixi173 – 181Combined sources9
    Beta strandi185 – 188Combined sources4
    Helixi192 – 202Combined sources11
    Beta strandi204 – 212Combined sources9
    Beta strandi217 – 219Combined sources3
    Helixi223 – 241Combined sources19
    Beta strandi247 – 250Combined sources4
    Beta strandi259 – 263Combined sources5
    Helixi268 – 280Combined sources13
    Turni281 – 285Combined sources5
    Beta strandi290 – 293Combined sources4
    Helixi297 – 300Combined sources4
    Helixi301 – 303Combined sources3
    Beta strandi304 – 315Combined sources12
    Beta strandi320 – 325Combined sources6
    Turni328 – 330Combined sources3
    Helixi333 – 337Combined sources5
    Beta strandi343 – 347Combined sources5
    Beta strandi352 – 358Combined sources7
    Beta strandi360 – 362Combined sources3
    Beta strandi367 – 375Combined sources9
    Beta strandi382 – 386Combined sources5
    Beta strandi389 – 392Combined sources4
    Helixi393 – 395Combined sources3
    Turni399 – 401Combined sources3
    Beta strandi406 – 411Combined sources6
    Beta strandi414 – 419Combined sources6
    Helixi424 – 427Combined sources4
    Turni428 – 430Combined sources3
    Helixi435 – 437Combined sources3

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiQ58497.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni294 – 297Pyridoxal phosphate bindingUniRule annotation1 Publication4

    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

    CDDicd06828. PLPDE_III_DapDC. 1 hit.
    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1TUFX-ray2.40A/B5-438[»]
    1TWIX-ray2.00A/B/C/D6-438[»]
    ProteinModelPortaliQ58497.
    SMRiQ58497.
    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

    CDDicd06828. PLPDE_III_DapDC. 1 hit.
    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: November 2, 2016
    This is version 115 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.