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P00861

- DCDA_ECOLI

UniProt

P00861 - DCDA_ECOLI

Protein

Diaminopimelate decarboxylase

Gene

lysA

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 134 (01 Oct 2014)
      Sequence version 1 (21 Jul 1986)
      Previous versions | rss
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    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 phosphate.2 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

    Pathwayi

    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

    1. diaminopimelate decarboxylase activity Source: EcoCyc
    2. protein binding Source: IntAct
    3. pyridoxal phosphate binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. lysine biosynthetic process via diaminopimelate Source: UniProtKB-HAMAP

    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: Chromosome, UP000000625: 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

    Gene expression databases

    GenevestigatoriP00861.

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

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    KOiK01586.
    OMAiVFTQQAG.
    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

    MPHSLFSTDT DLTAENLLRL PAEFGCPVWV YDAQIIRRQI AALKQFDVVR    50
    FAQKACSNIH ILRLMREQGV KVDSVSLGEI ERALAAGYNP QTHPDDIVFT 100
    ADVIDQATLE RVSELQIPVN AGSVDMLDQL GQVSPGHRVW LRVNPGFGHG 150
    HSQKTNTGGE NSKHGIWYTD LPAALDVIQR HHLQLVGIHM HIGSGVDYAH 200
    LEQVCGAMVR QVIEFGQDLQ AISAGGGLSV PYQQGEEAVD TEHYYGLWNA 250
    AREQIARHLG HPVKLEIEPG RFLVAQSGVL ITQVRSVKQM GSRHFVLVDA 300
    GFNDLMRPAM YGSYHHISAL AADGRSLEHA PTVETVVAGP LCESGDVFTQ 350
    QEGGNVETRA LPEVKAGDYL VLHDTGAYGA SMSSNYNSRP LLPEVLFDNG 400
    QARLIRRRQT IEELLALELL 420
    Length:420
    Mass (Da):46,177
    Last modified:July 21, 1986 - v1
    Checksum:i0A26ABCFAF8462B5
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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.
    YP_491043.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75877; AAC75877; b2838.
    BAE76907; BAE76907; BAE76907.
    GeneIDi12932897.
    947313.
    KEGGiecj:Y75_p2772.
    eco:b2838.
    PATRICi32121094. VBIEscCol129921_2936.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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 .
    PIRi A01078. DCECD.
    RefSeqi NP_417315.1. NC_000913.3.
    YP_491043.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1KNW X-ray 2.10 A 1-420 [» ]
    1KO0 X-ray 2.20 A 1-420 [» ]
    ProteinModelPortali P00861.
    SMRi P00861. Positions 2-411.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-10132N.
    IntActi P00861. 9 interactions.
    MINTi MINT-1292495.
    STRINGi 511145.b2838.

    2D gel databases

    SWISS-2DPAGE P00861.

    Proteomic databases

    PaxDbi P00861.
    PRIDEi P00861.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC75877 ; AAC75877 ; b2838 .
    BAE76907 ; BAE76907 ; BAE76907 .
    GeneIDi 12932897.
    947313.
    KEGGi ecj:Y75_p2772.
    eco:b2838.
    PATRICi 32121094. VBIEscCol129921_2936.

    Organism-specific databases

    EchoBASEi EB0544.
    EcoGenei EG10549. lysA.

    Phylogenomic databases

    eggNOGi COG0019.
    HOGENOMi HOG000045070.
    KOi K01586.
    OMAi VFTQQAG.
    OrthoDBi EOG6Z9B18.
    PhylomeDBi P00861.

    Enzyme and pathway databases

    UniPathwayi UPA00034 ; UER00027 .
    BioCyci EcoCyc:DIAMINOPIMDECARB-MONOMER.
    ECOL316407:JW2806-MONOMER.
    MetaCyc:DIAMINOPIMDECARB-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P00861.
    PROi P00861.

    Gene expression databases

    Genevestigatori P00861.

    Family and domain databases

    Gene3Di 2.40.37.10. 1 hit.
    3.20.20.10. 1 hit.
    HAMAPi MF_02120. LysA.
    InterProi 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.
    [Graphical view ]
    Pfami PF02784. Orn_Arg_deC_N. 1 hit.
    PF00278. Orn_DAP_Arg_deC. 1 hit.
    [Graphical view ]
    PRINTSi PR01181. DAPDCRBXLASE.
    PR01179. ODADCRBXLASE.
    SUPFAMi SSF50621. SSF50621. 1 hit.
    SSF51419. SSF51419. 1 hit.
    TIGRFAMsi TIGR01048. lysA. 1 hit.
    PROSITEi PS00878. ODR_DC_2_1. 1 hit.
    PS00879. ODR_DC_2_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 134 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