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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)2 Publications
  2. KM=1.07 mM for meso-2,6-diaminoheptanedioate (at pH 8)2 Publications

    pH dependencei

    Optimum pH is 6.7-6.8.1 Publication

    Pathway: 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), 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 sitei191 – 1911Substrate
    Binding sitei227 – 2271Pyridoxal phosphate; via amide nitrogen
    Binding sitei271 – 2711Substrate
    Binding sitei307 – 3071Substrate
    Binding sitei311 – 3111Substrate
    Active sitei342 – 3421Proton donorSequence Analysis
    Binding sitei343 – 3431Substrate
    Binding sitei378 – 3781Pyridoxal phosphate
    Binding sitei378 – 3781Substrate
    Binding sitei382 – 3821Substrate

    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 decarboxylase (EC:4.1.1.20)
    Short name:
    DAP decarboxylase
    Short name:
    DAPDC
    Gene namesi
    Name:lysA
    Ordered Locus Names:b2838, JW2806
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10549. lysA.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 420420Diaminopimelate decarboxylasePRO_0000149923Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei54 – 541N6-(pyridoxal phosphate)lysine

    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

    DIPiDIP-10132N.
    IntActiP00861. 9 interactions.
    MINTiMINT-1292495.
    STRINGi511145.b2838.

    Structurei

    Secondary structure

    1
    420
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni5 – 73Combined sources
    Beta strandi9 – 113Combined sources
    Helixi14 – 2411Combined sources
    Beta strandi26 – 327Combined sources
    Helixi33 – 419Combined sources
    Turni42 – 454Combined sources
    Beta strandi46 – 527Combined sources
    Helixi53 – 553Combined sources
    Helixi59 – 679Combined sources
    Beta strandi71 – 744Combined sources
    Helixi77 – 859Combined sources
    Turni90 – 923Combined sources
    Beta strandi96 – 1027Combined sources
    Helixi106 – 11510Combined sources
    Beta strandi119 – 1235Combined sources
    Helixi124 – 13310Combined sources
    Beta strandi138 – 1447Combined sources
    Beta strandi152 – 1554Combined sources
    Beta strandi157 – 1593Combined sources
    Beta strandi165 – 1673Combined sources
    Helixi168 – 1703Combined sources
    Helixi171 – 18010Combined sources
    Beta strandi184 – 1896Combined sources
    Helixi198 – 21518Combined sources
    Beta strandi220 – 2234Combined sources
    Helixi241 – 25919Combined sources
    Beta strandi264 – 2674Combined sources
    Helixi271 – 2744Combined sources
    Helixi275 – 2773Combined sources
    Beta strandi278 – 29013Combined sources
    Beta strandi293 – 2997Combined sources
    Turni302 – 3043Combined sources
    Helixi307 – 3115Combined sources
    Beta strandi317 – 3204Combined sources
    Beta strandi332 – 3387Combined sources
    Beta strandi340 – 3434Combined sources
    Beta strandi347 – 3504Combined sources
    Beta strandi359 – 3624Combined sources
    Beta strandi369 – 3724Combined sources
    Beta strandi376 – 3794Combined sources
    Helixi380 – 3823Combined sources
    Turni386 – 3883Combined sources
    Beta strandi394 – 3985Combined sources
    Beta strandi401 – 4066Combined sources
    Helixi411 – 4155Combined sources
    Turni416 – 4183Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1KNWX-ray2.10A1-420[»]
    1KO0X-ray2.20A1-420[»]
    ProteinModelPortaliP00861.
    SMRiP00861. Positions 2-411.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP00861.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni268 – 2714Pyridoxal phosphate binding

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0019.
    HOGENOMiHOG000045070.
    InParanoidiP00861.
    KOiK01586.
    OMAiVVGYICE.
    OrthoDBiEOG6Z9B18.
    PhylomeDBiP00861.

    Family and domain databases

    Gene3Di2.40.37.10. 1 hit.
    3.20.20.10. 1 hit.
    HAMAPiMF_02120. LysA.
    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.

    Genome annotation databases

    EnsemblBacteriaiAAC75877; AAC75877; b2838.
    BAE76907; BAE76907; BAE76907.
    GeneIDi947313.
    KEGGiecj:Y75_p2772.
    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.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1KNWX-ray2.10A1-420[»]
    1KO0X-ray2.20A1-420[»]
    ProteinModelPortaliP00861.
    SMRiP00861. Positions 2-411.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-10132N.
    IntActiP00861. 9 interactions.
    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:Y75_p2772.
    eco:b2838.
    PATRICi32121094. VBIEscCol129921_2936.

    Organism-specific databases

    EchoBASEiEB0544.
    EcoGeneiEG10549. lysA.

    Phylogenomic databases

    eggNOGiCOG0019.
    HOGENOMiHOG000045070.
    InParanoidiP00861.
    KOiK01586.
    OMAiVVGYICE.
    OrthoDBiEOG6Z9B18.
    PhylomeDBiP00861.

    Enzyme and pathway databases

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

    Miscellaneous databases

    EvolutionaryTraceiP00861.
    PROiP00861.

    Family and domain databases

    Gene3Di2.40.37.10. 1 hit.
    3.20.20.10. 1 hit.
    HAMAPiMF_02120. LysA.
    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...

    Publicationsi

    « Hide 'large scale' publications
    1. "Regulation of diaminopimelate decarboxylase synthesis in Escherichia coli. II. Nucleotide sequence of the lysA gene and its regulatory region."
      Stragier P., Danos O., Patte J.-C.
      J. Mol. Biol. 168:321-331(1983) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. "Purification and properties of diaminopimelate decarboxylase from Escherichia coli."
      White P.J., Kelly B.
      Biochem. J. 96:75-84(1965) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, PATHWAY.
      Strain: ATCC 9637 / CCM 2024 / DSM 1116 / NCIMB 8666 / NRRL B-766 / W.
    5. "Regulatory pattern of the Escherichia coli lysA gene: expression of chromosomal lysA-lacZ fusions."
      Stragier P., Borne F., Richaud F., Richaud C., Patte J.C.
      J. Bacteriol. 156:1198-1203(1983) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
    6. "Regulation of diaminopimelate decarboxylase synthesis in Escherichia coli. I. Identification of a lysR gene encoding an activator of the lysA gene."
      Stragier P., Richaud F., Borne F., Patte J.C.
      J. Mol. Biol. 168:307-320(1983) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
    7. "Escherichia coli proteome analysis using the gene-protein database."
      VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
      Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY 2D-GEL.
    8. "Crystallization of diaminopimelate decarboxylase from Escherichia coli, a stereospecific D-amino-acid decarboxylase."
      Momany C., Levdikov V., Blagova L., Crews K.
      Acta Crystallogr. D 58:549-552(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: CRYSTALLIZATION, FUNCTION, CATALYTIC ACTIVITY, COFACTOR.
    9. "The catalytic intermediate stabilized by a 'down' active site loop for diaminopimelate decarboxylase from Helicobacter pylori. Enzymatic characterization with crystal structure analysis."
      Hu T., Wu D., Chen J., Ding J., Jiang H., Shen X.
      J. Biol. Chem. 283:21284-21293(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS.
      Strain: K12 / JM109 / ATCC 53323.
    10. "Diaminopimelate decarboxylase uses a versatile active site for stereospecific decarboxylation."
      Levdikov V., Blagova L., Bose N., Momany C.
      Submitted (FEB-2009) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEXES WITH PYRIDOXAL PHOSPHATE AND LYSINE.

    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: June 24, 2015
    This is version 139 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

    External Data

    Dasty 3

    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 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.