DCDA_ECOLI
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 03-AUG-2022, entry version 177.
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; Proteobacteria; 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 SWISS-2DPAGE; P00861; -.
DR jPOST; P00861; -.
DR PaxDb; P00861; -.
DR PRIDE; P00861; -.
DR EnsemblBacteria; AAC75877; AAC75877; b2838.
DR EnsemblBacteria; BAE76907; BAE76907; BAE76907.
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 PhylomeDB; P00861; -.
DR BioCyc; EcoCyc:DIAMINOPIMDECARB-MON; -.
DR BioCyc; MetaCyc:DIAMINOPIMDECARB-MON; -.
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: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; 2.40.37.10; -; 1.
DR Gene3D; 3.20.20.10; -; 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 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; SSF50621; 1.
DR SUPFAM; SSF51419; SSF51419; 1.
DR TIGRFAMs; TIGR01048; lysA; 1.
DR PROSITE; PS00878; ODR_DC_2_1; 1.
DR PROSITE; PS00879; ODR_DC_2_2; 1.
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
