ID   DCDA_ECOLI              Reviewed;         420 AA.
AC   P00861; Q2M9Z9;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   21-JUL-1986, sequence version 1.
DT   24-JAN-2024, entry version 185.
DE   RecName: Full=Diaminopimelate decarboxylase {ECO:0000255|HAMAP-Rule:MF_02120};
DE            Short=DAP decarboxylase {ECO:0000255|HAMAP-Rule:MF_02120};
DE            Short=DAPDC {ECO:0000255|HAMAP-Rule:MF_02120};
DE            EC=4.1.1.20 {ECO:0000255|HAMAP-Rule:MF_02120, ECO:0000269|PubMed:11856852, ECO:0000269|PubMed:14343156, ECO:0000269|PubMed:18508763};
GN   Name=lysA {ECO:0000255|HAMAP-Rule:MF_02120};
GN   OrderedLocusNames=b2838, JW2806;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=6350601; DOI=10.1016/s0022-2836(83)80021-7;
RA   Stragier P., Danos O., Patte J.-C.;
RT   "Regulation of diaminopimelate decarboxylase synthesis in Escherichia coli.
RT   II. Nucleotide sequence of the lysA gene and its regulatory region.";
RL   J. Mol. Biol. 168:321-331(1983).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA   Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA   Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA   Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA   Shao Y.;
RT   "The complete genome sequence of Escherichia coli K-12.";
RL   Science 277:1453-1462(1997).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=16738553; DOI=10.1038/msb4100049;
RA   Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA   Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT   "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT   and W3110.";
RL   Mol. Syst. Biol. 2:E1-E5(2006).
RN   [4]
RP   FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR, ACTIVITY
RP   REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, AND PATHWAY.
RC   STRAIN=ATCC 9637 / CCM 2024 / DSM 1116 / NCIMB 8666 / NRRL B-766 / W;
RX   PubMed=14343156; DOI=10.1042/bj0960075;
RA   White P.J., Kelly B.;
RT   "Purification and properties of diaminopimelate decarboxylase from
RT   Escherichia coli.";
RL   Biochem. J. 96:75-84(1965).
RN   [5]
RP   INDUCTION.
RX   PubMed=6417111; DOI=10.1128/jb.156.3.1198-1203.1983;
RA   Stragier P., Borne F., Richaud F., Richaud C., Patte J.C.;
RT   "Regulatory pattern of the Escherichia coli lysA gene: expression of
RT   chromosomal lysA-lacZ fusions.";
RL   J. Bacteriol. 156:1198-1203(1983).
RN   [6]
RP   INDUCTION.
RX   PubMed=6411928; DOI=10.1016/s0022-2836(83)80020-5;
RA   Stragier P., Richaud F., Borne F., Patte J.C.;
RT   "Regulation of diaminopimelate decarboxylase synthesis in Escherichia coli.
RT   I. Identification of a lysR gene encoding an activator of the lysA gene.";
RL   J. Mol. Biol. 168:307-320(1983).
RN   [7]
RP   IDENTIFICATION BY 2D-GEL.
RX   PubMed=9298644; DOI=10.1002/elps.1150180805;
RA   VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT   "Escherichia coli proteome analysis using the gene-protein database.";
RL   Electrophoresis 18:1243-1251(1997).
RN   [8]
RP   CRYSTALLIZATION, FUNCTION, CATALYTIC ACTIVITY, AND COFACTOR.
RX   PubMed=11856852; DOI=10.1107/s0907444902000148;
RA   Momany C., Levdikov V., Blagova L., Crews K.;
RT   "Crystallization of diaminopimelate decarboxylase from Escherichia coli, a
RT   stereospecific D-amino-acid decarboxylase.";
RL   Acta Crystallogr. D 58:549-552(2002).
RN   [9]
RP   FUNCTION, CATALYTIC ACTIVITY, AND KINETIC PARAMETERS.
RC   STRAIN=K12 / JM109 / ATCC 53323;
RX   PubMed=18508763; DOI=10.1074/jbc.m801823200;
RA   Hu T., Wu D., Chen J., Ding J., Jiang H., Shen X.;
RT   "The catalytic intermediate stabilized by a 'down' active site loop for
RT   diaminopimelate decarboxylase from Helicobacter pylori. Enzymatic
RT   characterization with crystal structure analysis.";
RL   J. Biol. Chem. 283:21284-21293(2008).
RN   [10]
RP   X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEXES WITH PYRIDOXAL PHOSPHATE
RP   AND LYSINE.
RA   Levdikov V., Blagova L., Bose N., Momany C.;
RT   "Diaminopimelate decarboxylase uses a versatile active site for
RT   stereospecific decarboxylation.";
RL   Submitted (FEB-2009) to the PDB data bank.
CC   -!- FUNCTION: Specifically catalyzes the decarboxylation of meso-
CC       diaminopimelate (meso-DAP) to L-lysine. Is not active against the
CC       DD- or LL-isomers of diaminopimelate. {ECO:0000269|PubMed:11856852,
CC       ECO:0000269|PubMed:14343156, ECO:0000269|PubMed:18508763}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=H(+) + meso-2,6-diaminoheptanedioate = CO2 + L-lysine;
CC         Xref=Rhea:RHEA:15101, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC         ChEBI:CHEBI:32551, ChEBI:CHEBI:57791; EC=4.1.1.20;
CC         Evidence={ECO:0000269|PubMed:11856852, ECO:0000269|PubMed:14343156,
CC         ECO:0000269|PubMed:18508763};
CC   -!- COFACTOR:
CC       Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC         Evidence={ECO:0000269|PubMed:11856852, ECO:0000269|PubMed:14343156};
CC   -!- ACTIVITY REGULATION: Is activated by 2,3-dimercaptopropan-1-ol.
CC       {ECO:0000269|PubMed:14343156}.
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=1.7 mM for meso-2,6-diaminoheptanedioate (at pH 6.8 and 37 degrees
CC         Celsius) {ECO:0000269|PubMed:14343156};
CC         KM=1.07 mM for meso-2,6-diaminoheptanedioate (at pH 8)
CC         {ECO:0000269|PubMed:18508763};
CC       pH dependence:
CC         Optimum pH is 6.7-6.8. {ECO:0000269|PubMed:14343156};
CC   -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC       pathway; L-lysine from DL-2,6-diaminopimelate: step 1/1.
CC       {ECO:0000269|PubMed:14343156}.
CC   -!- INTERACTION:
CC       P00861; P0AE88: cpxR; NbExp=4; IntAct=EBI-553837, EBI-550918;
CC   -!- INDUCTION: Up-regulated by LysR. Repressed in the presence of lysine.
CC       {ECO:0000269|PubMed:6411928, ECO:0000269|PubMed:6417111}.
CC   -!- SIMILARITY: Belongs to the Orn/Lys/Arg decarboxylase class-II family.
CC       LysA subfamily. {ECO:0000255|HAMAP-Rule:MF_02120}.
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DR   EMBL; J01614; AAA83861.1; -; Genomic_DNA.
DR   EMBL; U29581; AAB40485.1; -; Genomic_DNA.
DR   EMBL; U00096; AAC75877.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAE76907.1; -; Genomic_DNA.
DR   PIR; A01078; DCECD.
DR   RefSeq; NP_417315.1; NC_000913.3.
DR   RefSeq; WP_001120711.1; NZ_SSUV01000026.1.
DR   PDB; 1KNW; X-ray; 2.10 A; A=1-420.
DR   PDB; 1KO0; X-ray; 2.20 A; A=1-420.
DR   PDBsum; 1KNW; -.
DR   PDBsum; 1KO0; -.
DR   AlphaFoldDB; P00861; -.
DR   SMR; P00861; -.
DR   BioGRID; 4261891; 8.
DR   BioGRID; 851640; 2.
DR   DIP; DIP-10132N; -.
DR   IntAct; P00861; 9.
DR   STRING; 511145.b2838; -.
DR   DrugBank; DB03814; 2-(N-morpholino)ethanesulfonic acid.
DR   DrugBank; DB03252; D-Lysine.
DR   jPOST; P00861; -.
DR   PaxDb; 511145-b2838; -.
DR   EnsemblBacteria; AAC75877; AAC75877; b2838.
DR   GeneID; 947313; -.
DR   KEGG; ecj:JW2806; -.
DR   KEGG; eco:b2838; -.
DR   PATRIC; fig|1411691.4.peg.3896; -.
DR   EchoBASE; EB0544; -.
DR   eggNOG; COG0019; Bacteria.
DR   HOGENOM; CLU_026444_0_2_6; -.
DR   InParanoid; P00861; -.
DR   OMA; HGNAKSP; -.
DR   OrthoDB; 9802241at2; -.
DR   PhylomeDB; P00861; -.
DR   BioCyc; EcoCyc:DIAMINOPIMDECARB-MONOMER; -.
DR   BioCyc; MetaCyc:DIAMINOPIMDECARB-MONOMER; -.
DR   BRENDA; 4.1.1.20; 2026.
DR   SABIO-RK; P00861; -.
DR   UniPathway; UPA00034; UER00027.
DR   EvolutionaryTrace; P00861; -.
DR   PRO; PR:P00861; -.
DR   Proteomes; UP000000318; Chromosome.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0008836; F:diaminopimelate decarboxylase activity; IDA:EcoCyc.
DR   GO; GO:0042803; F:protein homodimerization activity; IDA:EcoCyc.
DR   GO; GO:0030170; F:pyridoxal phosphate binding; IDA:EcoCyc.
DR   GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IMP:EcoCyc.
DR   CDD; cd06828; PLPDE_III_DapDC; 1.
DR   Gene3D; 3.20.20.10; Alanine racemase; 1.
DR   HAMAP; MF_02120; LysA; 1.
DR   InterPro; IPR009006; Ala_racemase/Decarboxylase_C.
DR   InterPro; IPR002986; DAP_deCOOHase_LysA.
DR   InterPro; IPR022643; De-COase2_C.
DR   InterPro; IPR022657; De-COase2_CS.
DR   InterPro; IPR022644; De-COase2_N.
DR   InterPro; IPR022653; De-COase2_pyr-phos_BS.
DR   InterPro; IPR000183; Orn/DAP/Arg_de-COase.
DR   InterPro; IPR029066; PLP-binding_barrel.
DR   NCBIfam; TIGR01048; lysA; 1.
DR   PANTHER; PTHR43727; DIAMINOPIMELATE DECARBOXYLASE; 1.
DR   PANTHER; PTHR43727:SF2; DIAMINOPIMELATE DECARBOXYLASE 1, CHLOROPLASTIC-RELATED; 1.
DR   Pfam; PF02784; Orn_Arg_deC_N; 1.
DR   Pfam; PF00278; Orn_DAP_Arg_deC; 1.
DR   PRINTS; PR01181; DAPDCRBXLASE.
DR   PRINTS; PR01179; ODADCRBXLASE.
DR   SUPFAM; SSF50621; Alanine racemase C-terminal domain-like; 1.
DR   SUPFAM; SSF51419; PLP-binding barrel; 1.
DR   PROSITE; PS00878; ODR_DC_2_1; 1.
DR   PROSITE; PS00879; ODR_DC_2_2; 1.
DR   SWISS-2DPAGE; P00861; -.
PE   1: Evidence at protein level;
KW   3D-structure; Amino-acid biosynthesis; Decarboxylase; Lyase;
KW   Lysine biosynthesis; Pyridoxal phosphate; Reference proteome.
FT   CHAIN           1..420
FT                   /note="Diaminopimelate decarboxylase"
FT                   /id="PRO_0000149923"
FT   ACT_SITE        342
FT                   /note="Proton donor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT   BINDING         191
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000305|Ref.10"
FT   BINDING         227
FT                   /ligand="pyridoxal 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:597326"
FT                   /evidence="ECO:0000269|Ref.10"
FT   BINDING         268..271
FT                   /ligand="pyridoxal 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:597326"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02120,
FT                   ECO:0000269|Ref.10"
FT   BINDING         271
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000305|Ref.10"
FT   BINDING         307
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000305|Ref.10"
FT   BINDING         311
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000305|Ref.10"
FT   BINDING         343
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000305|Ref.10"
FT   BINDING         378
FT                   /ligand="pyridoxal 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:597326"
FT                   /evidence="ECO:0000269|Ref.10"
FT   BINDING         378
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT   MOD_RES         54
FT                   /note="N6-(pyridoxal phosphate)lysine"
FT                   /evidence="ECO:0000269|Ref.10"
FT   TURN            5..7
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          9..11
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   HELIX           14..24
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          26..32
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   HELIX           33..41
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   TURN            42..45
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          46..52
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   HELIX           53..55
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   HELIX           59..67
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          71..74
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   HELIX           77..85
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   TURN            90..92
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          96..102
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   HELIX           106..115
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          119..123
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   HELIX           124..133
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          138..144
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          152..155
FT                   /evidence="ECO:0007829|PDB:1KO0"
FT   STRAND          157..159
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          165..167
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   HELIX           168..170
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   HELIX           171..180
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          184..189
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   HELIX           198..215
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          220..223
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   HELIX           241..259
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          264..267
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   HELIX           271..274
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   HELIX           275..277
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          278..290
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          293..299
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   TURN            302..304
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   HELIX           307..311
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          317..320
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          332..338
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          340..343
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          347..350
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          359..362
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          369..372
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          376..379
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   HELIX           380..382
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   TURN            386..388
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          394..398
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   STRAND          401..406
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   HELIX           411..415
FT                   /evidence="ECO:0007829|PDB:1KNW"
FT   TURN            416..418
FT                   /evidence="ECO:0007829|PDB:1KNW"
SQ   SEQUENCE   420 AA;  46177 MW;  0A26ABCFAF8462B5 CRC64;
     MPHSLFSTDT DLTAENLLRL PAEFGCPVWV YDAQIIRRQI AALKQFDVVR FAQKACSNIH
     ILRLMREQGV KVDSVSLGEI ERALAAGYNP QTHPDDIVFT ADVIDQATLE RVSELQIPVN
     AGSVDMLDQL GQVSPGHRVW LRVNPGFGHG HSQKTNTGGE NSKHGIWYTD LPAALDVIQR
     HHLQLVGIHM HIGSGVDYAH LEQVCGAMVR QVIEFGQDLQ AISAGGGLSV PYQQGEEAVD
     TEHYYGLWNA AREQIARHLG HPVKLEIEPG RFLVAQSGVL ITQVRSVKQM GSRHFVLVDA
     GFNDLMRPAM YGSYHHISAL AADGRSLEHA PTVETVVAGP LCESGDVFTQ QEGGNVETRA
     LPEVKAGDYL VLHDTGAYGA SMSSNYNSRP LLPEVLFDNG QARLIRRRQT IEELLALELL
//