DCDA_ECOLW
ID DCDA_ECOLW Reviewed; 420 AA.
AC E0IWI3; H9Y5F7;
DT 27-JUL-2011, integrated into UniProtKB/Swiss-Prot.
DT 02-NOV-2010, sequence version 1.
DT 03-AUG-2022, entry version 55.
DE RecName: Full=Diaminopimelate decarboxylase;
DE Short=DAP decarboxylase;
DE Short=DAPDC;
DE EC=4.1.1.20;
GN Name=lysA; OrderedLocusNames=ECW_m3083, WFL_15045;
GN ORFNames=EschWDRAFT_0728;
OS Escherichia coli (strain ATCC 9637 / CCM 2024 / DSM 1116 / LMG 11080 / NBRC
OS 13500 / NCIMB 8666 / NRRL B-766 / W).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=566546;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 9637 / CCM 2024 / DSM 1116 / LMG 11080 / NBRC 13500 / NCIMB
RC 8666 / NRRL B-766 / W;
RG US DOE Joint Genome Institute (JGI-PGF);
RA Lucas S., Copeland A., Lapidus A., Cheng J.-F., Bruce D., Goodwin L.,
RA Pitluck S., Land M.L., Hauser L., Chang Y.-J., Jeffries C., Tremaine M.,
RA Landick R., Keating D., Woyke T.J.;
RT "The draft genome of Escherichia coli W.";
RL Submitted (JUL-2010) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 9637 / CCM 2024 / DSM 1116 / LMG 11080 / NBRC 13500 / NCIMB
RC 8666 / NRRL B-766 / W;
RX PubMed=21208457; DOI=10.1186/1471-2164-12-9;
RA Archer C.T., Kim J.F., Jeong H., Park J.H., Vickers C.E., Lee S.Y.,
RA Nielsen L.K.;
RT "The genome sequence of E. coli W (ATCC 9637): comparative genome analysis
RT and an improved genome-scale reconstruction of E. coli.";
RL BMC Genomics 12:9-9(2011).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 9637 / CCM 2024 / DSM 1116 / LMG 11080 / NBRC 13500 / NCIMB
RC 8666 / NRRL B-766 / W;
RX PubMed=22075923; DOI=10.1007/s10295-011-1052-2;
RA Turner P.C., Yomano L.P., Jarboe L.R., York S.W., Baggett C.L.,
RA Moritz B.E., Zentz E.B., Shanmugam K.T., Ingram L.O.;
RT "Optical mapping and sequencing of the Escherichia coli KO11 genome reveal
RT extensive chromosomal rearrangements, and multiple tandem copies of the
RT Zymomonas mobilis pdc and adhB genes.";
RL J. Ind. Microbiol. Biotechnol. 39:629-639(2012).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR, ACTIVITY
RP REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, AND PATHWAY.
RC STRAIN=ATCC 9637 / CCM 2024 / DSM 1116 / LMG 11080 / NBRC 13500 / NCIMB
RC 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).
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:14343156}.
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:14343156};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={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 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 -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the Orn/Lys/Arg decarboxylase class-II family.
CC LysA subfamily. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AEDF01000002; EFN39941.1; -; Genomic_DNA.
DR EMBL; CP002185; ADT76472.1; -; Genomic_DNA.
DR EMBL; CP002967; AFH12659.1; -; Genomic_DNA.
DR RefSeq; WP_001120711.1; NZ_WBMH01000034.1.
DR AlphaFoldDB; E0IWI3; -.
DR SMR; E0IWI3; -.
DR EnsemblBacteria; ADT76472; ADT76472; ECW_m3083.
DR KEGG; ell:WFL_15045; -.
DR KEGG; elw:ECW_m3083; -.
DR PATRIC; fig|566546.30.peg.3131; -.
DR HOGENOM; CLU_026444_0_2_6; -.
DR OMA; HGNAKSP; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000008525; Chromosome.
DR GO; GO:0008836; F:diaminopimelate decarboxylase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IEA:UniProtKB-UniRule.
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 Amino-acid biosynthesis; Decarboxylase; Lyase; Lysine biosynthesis;
KW Pyridoxal phosphate.
FT CHAIN 1..420
FT /note="Diaminopimelate decarboxylase"
FT /id="PRO_0000411128"
FT BINDING 227
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT BINDING 268..271
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT BINDING 271
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 307
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 311
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 343
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 378
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT BINDING 378
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT MOD_RES 54
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250"
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
