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Protein

Diaminopimelate decarboxylase

Gene

lysA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine. Is not active against the DD- or LL-isomers of diaminopimelate.3 Publications

Catalytic activityi

Meso-2,6-diaminoheptanedioate = L-lysine + CO2.3 Publications

Cofactori

pyridoxal 5'-phosphate2 Publications

Enzyme regulationi

Is activated by 2,3-dimercaptopropan-1-ol.1 Publication

Kineticsi

  1. KM=1.7 mM for meso-2,6-diaminoheptanedioate (at pH 6.8 and 37 degrees Celsius)1 Publication
  2. KM=1.07 mM for meso-2,6-diaminoheptanedioate (at pH 8)1 Publication

    pH dependencei

    Optimum pH is 6.7-6.8.1 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.1 Publication
    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 sitei191Substrate1 Publication1
    Binding sitei227Pyridoxal phosphate; via amide nitrogen1 Publication1
    Binding sitei271Substrate1 Publication1
    Binding sitei307Substrate1 Publication1
    Binding sitei311Substrate1 Publication1
    Active sitei342Proton donorUniRule annotation1
    Binding sitei343Substrate1 Publication1
    Binding sitei378Pyridoxal phosphate1 Publication1
    Binding sitei378SubstrateUniRule annotation1

    GO - Molecular functioni

    • diaminopimelate decarboxylase activity Source: EcoCyc
    • pyridoxal phosphate binding Source: EcoCyc

    GO - Biological processi

    • lysine biosynthetic process via diaminopimelate Source: EcoCyc

    Keywordsi

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

    Enzyme and pathway databases

    BioCyciEcoCyc:DIAMINOPIMDECARB-MONOMER
    MetaCyc:DIAMINOPIMDECARB-MONOMER
    UniPathwayiUPA00034; UER00027

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Diaminopimelate decarboxylaseUniRule annotation (EC:4.1.1.20UniRule annotation3 Publications)
    Short name:
    DAP decarboxylaseUniRule annotation
    Short name:
    DAPDCUniRule annotation
    Gene namesi
    Name:lysAUniRule annotation
    Ordered Locus Names:b2838, JW2806
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10549 lysA

    Pathology & Biotechi

    Chemistry databases

    DrugBankiDB03814 2-(N-Morpholino)-Ethanesulfonic Acid
    DB03252 D-Lysine

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001499231 – 420Diaminopimelate decarboxylaseAdd BLAST420

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei54N6-(pyridoxal phosphate)lysine1 Publication1

    Proteomic databases

    PaxDbiP00861
    PRIDEiP00861

    2D gel databases

    SWISS-2DPAGEiP00861

    Expressioni

    Inductioni

    Up-regulated by LysR. Repressed in the presence of lysine.2 Publications

    Interactioni

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    cpxRP0AE884EBI-553837,EBI-550918

    Protein-protein interaction databases

    BioGridi4261891, 8 interactors
    DIPiDIP-10132N
    IntActiP00861, 9 interactors
    STRINGi316385.ECDH10B_3010

    Structurei

    Secondary structure

    1420
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Turni5 – 7Combined sources3
    Beta strandi9 – 11Combined sources3
    Helixi14 – 24Combined sources11
    Beta strandi26 – 32Combined sources7
    Helixi33 – 41Combined sources9
    Turni42 – 45Combined sources4
    Beta strandi46 – 52Combined sources7
    Helixi53 – 55Combined sources3
    Helixi59 – 67Combined sources9
    Beta strandi71 – 74Combined sources4
    Helixi77 – 85Combined sources9
    Turni90 – 92Combined sources3
    Beta strandi96 – 102Combined sources7
    Helixi106 – 115Combined sources10
    Beta strandi119 – 123Combined sources5
    Helixi124 – 133Combined sources10
    Beta strandi138 – 144Combined sources7
    Beta strandi152 – 155Combined sources4
    Beta strandi157 – 159Combined sources3
    Beta strandi165 – 167Combined sources3
    Helixi168 – 170Combined sources3
    Helixi171 – 180Combined sources10
    Beta strandi184 – 189Combined sources6
    Helixi198 – 215Combined sources18
    Beta strandi220 – 223Combined sources4
    Helixi241 – 259Combined sources19
    Beta strandi264 – 267Combined sources4
    Helixi271 – 274Combined sources4
    Helixi275 – 277Combined sources3
    Beta strandi278 – 290Combined sources13
    Beta strandi293 – 299Combined sources7
    Turni302 – 304Combined sources3
    Helixi307 – 311Combined sources5
    Beta strandi317 – 320Combined sources4
    Beta strandi332 – 338Combined sources7
    Beta strandi340 – 343Combined sources4
    Beta strandi347 – 350Combined sources4
    Beta strandi359 – 362Combined sources4
    Beta strandi369 – 372Combined sources4
    Beta strandi376 – 379Combined sources4
    Helixi380 – 382Combined sources3
    Turni386 – 388Combined sources3
    Beta strandi394 – 398Combined sources5
    Beta strandi401 – 406Combined sources6
    Helixi411 – 415Combined sources5
    Turni416 – 418Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1KNWX-ray2.10A1-420[»]
    1KO0X-ray2.20A1-420[»]
    ProteinModelPortaliP00861
    SMRiP00861
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP00861

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni268 – 271Pyridoxal phosphate bindingUniRule annotation1 Publication4

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiENOG4105CU5 Bacteria
    COG0019 LUCA
    HOGENOMiHOG000045070
    InParanoidiP00861
    KOiK01586
    OMAiVVGYICE
    PhylomeDBiP00861

    Family and domain databases

    CDDicd06828 PLPDE_III_DapDC, 1 hit
    Gene3Di2.40.37.10, 2 hits
    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
    PANTHERiPTHR43727:SF2 PTHR43727:SF2, 1 hit
    PfamiView protein in Pfam
    PF02784 Orn_Arg_deC_N, 1 hit
    PF00278 Orn_DAP_Arg_deC, 1 hit
    PRINTSiPR01181 DAPDCRBXLASE
    PR01179 ODADCRBXLASE
    SUPFAMiSSF50621 SSF50621, 1 hit
    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

    Sequencei

    Sequence statusi: Complete.

    P00861-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MPHSLFSTDT DLTAENLLRL PAEFGCPVWV YDAQIIRRQI AALKQFDVVR
    60 70 80 90 100
    FAQKACSNIH ILRLMREQGV KVDSVSLGEI ERALAAGYNP QTHPDDIVFT
    110 120 130 140 150
    ADVIDQATLE RVSELQIPVN AGSVDMLDQL GQVSPGHRVW LRVNPGFGHG
    160 170 180 190 200
    HSQKTNTGGE NSKHGIWYTD LPAALDVIQR HHLQLVGIHM HIGSGVDYAH
    210 220 230 240 250
    LEQVCGAMVR QVIEFGQDLQ AISAGGGLSV PYQQGEEAVD TEHYYGLWNA
    260 270 280 290 300
    AREQIARHLG HPVKLEIEPG RFLVAQSGVL ITQVRSVKQM GSRHFVLVDA
    310 320 330 340 350
    GFNDLMRPAM YGSYHHISAL AADGRSLEHA PTVETVVAGP LCESGDVFTQ
    360 370 380 390 400
    QEGGNVETRA LPEVKAGDYL VLHDTGAYGA SMSSNYNSRP LLPEVLFDNG
    410 420
    QARLIRRRQT IEELLALELL
    Length:420
    Mass (Da):46,177
    Last modified:July 21, 1986 - v1
    Checksum:i0A26ABCFAF8462B5
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    J01614 Genomic DNA Translation: AAA83861.1
    U29581 Genomic DNA Translation: AAB40485.1
    U00096 Genomic DNA Translation: AAC75877.1
    AP009048 Genomic DNA Translation: BAE76907.1
    PIRiA01078 DCECD
    RefSeqiNP_417315.1, NC_000913.3
    WP_001120711.1, NZ_LN832404.1

    Genome annotation databases

    EnsemblBacteriaiAAC75877; AAC75877; b2838
    BAE76907; BAE76907; BAE76907
    GeneIDi947313
    KEGGiecj:JW2806
    eco:b2838
    PATRICifig|1411691.4.peg.3896

    Similar proteinsi

    Entry informationi

    Entry nameiDCDA_ECOLI
    AccessioniPrimary (citable) accession number: P00861
    Secondary accession number(s): Q2M9Z9
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: July 21, 1986
    Last modified: March 28, 2018
    This is version 154 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome
    UniProt is an ELIXIR core data resource
    Main funding by: National Institutes of Health