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Protein

Diaminopimelate decarboxylase

Gene

lysA

Organism
Escherichia coli (strain K12)
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. 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: UniProtKB-HAMAP

    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

    BioCyciEcoCyc:DIAMINOPIMDECARB-MONOMER.
    ECOL316407:JW2806-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.

    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-2DPAGEP00861.

    Expressioni

    Inductioni

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

    Interactioni

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    cpxRP0AE882EBI-553837,EBI-550918

    Protein-protein interaction databases

    BioGridi4261891. 8 interactors.
    DIPiDIP-10132N.
    IntActiP00861. 9 interactors.
    MINTiMINT-1292495.
    STRINGi511145.b2838.

    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.
    OMAiNISVGHI.
    PhylomeDBiP00861.

    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. 1 hit.
    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.

    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.
    PATRICi32121094. VBIEscCol129921_2936.

    Cross-referencesi

    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.

    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...

    Protein-protein interaction databases

    BioGridi4261891. 8 interactors.
    DIPiDIP-10132N.
    IntActiP00861. 9 interactors.
    MINTiMINT-1292495.
    STRINGi511145.b2838.

    2D gel databases

    SWISS-2DPAGEP00861.

    Proteomic databases

    PaxDbiP00861.
    PRIDEiP00861.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75877; AAC75877; b2838.
    BAE76907; BAE76907; BAE76907.
    GeneIDi947313.
    KEGGiecj:JW2806.
    eco:b2838.
    PATRICi32121094. VBIEscCol129921_2936.

    Organism-specific databases

    EchoBASEiEB0544.
    EcoGeneiEG10549. lysA.

    Phylogenomic databases

    eggNOGiENOG4105CU5. Bacteria.
    COG0019. LUCA.
    HOGENOMiHOG000045070.
    InParanoidiP00861.
    KOiK01586.
    OMAiNISVGHI.
    PhylomeDBiP00861.

    Enzyme and pathway databases

    UniPathwayiUPA00034; UER00027.
    BioCyciEcoCyc:DIAMINOPIMDECARB-MONOMER.
    ECOL316407:JW2806-MONOMER.
    MetaCyc:DIAMINOPIMDECARB-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP00861.
    PROiP00861.

    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. 1 hit.
    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_ECOLI
    AccessioniPrimary (citable) accession number: P00861
    Secondary accession number(s): Q2M9Z9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: July 21, 1986
    Last modified: November 2, 2016
    This is version 146 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. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    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.