DCDA_COREF
ID DCDA_COREF Reviewed; 459 AA.
AC Q8RQM6;
DT 01-NOV-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 03-AUG-2022, entry version 115.
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};
GN Name=lysA {ECO:0000255|HAMAP-Rule:MF_02120}; OrderedLocusNames=CE1277;
OS Corynebacterium efficiens (strain DSM 44549 / YS-314 / AJ 12310 / JCM 11189
OS / NBRC 100395).
OC Bacteria; Actinobacteria; Corynebacteriales; Corynebacteriaceae;
OC Corynebacterium.
OX NCBI_TaxID=196164;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=DSM 44549 / YS-314 / AJ 12310 / JCM 11189 / NBRC 100395;
RA Itaya H., Kimura E., Kawahara Y., Sugimoto S.;
RT "lysA of Corynebacterium efficiens.";
RL Submitted (APR-2002) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 44549 / YS-314 / AJ 12310 / JCM 11189 / NBRC 100395;
RX PubMed=12840036; DOI=10.1101/gr.1285603;
RA Nishio Y., Nakamura Y., Kawarabayasi Y., Usuda Y., Kimura E., Sugimoto S.,
RA Matsui K., Yamagishi A., Kikuchi H., Ikeo K., Gojobori T.;
RT "Comparative complete genome sequence analysis of the amino acid
RT replacements responsible for the thermostability of Corynebacterium
RT efficiens.";
RL Genome Res. 13:1572-1579(2003).
CC -!- FUNCTION: Specifically catalyzes the decarboxylation of meso-
CC diaminopimelate (meso-DAP) to L-lysine. {ECO:0000255|HAMAP-
CC Rule:MF_02120}.
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:0000255|HAMAP-Rule:MF_02120};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02120};
CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC pathway; L-lysine from DL-2,6-diaminopimelate: step 1/1.
CC {ECO:0000255|HAMAP-Rule:MF_02120}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_02120}.
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; AB083132; BAB88825.1; -; Genomic_DNA.
DR EMBL; BA000035; BAC18087.1; -; Genomic_DNA.
DR RefSeq; WP_006769238.1; NZ_GG700686.1.
DR AlphaFoldDB; Q8RQM6; -.
DR SMR; Q8RQM6; -.
DR STRING; 196164.23493116; -.
DR EnsemblBacteria; BAC18087; BAC18087; BAC18087.
DR KEGG; cef:CE1277; -.
DR eggNOG; COG0019; Bacteria.
DR HOGENOM; CLU_026444_0_1_11; -.
DR OMA; YCRSMAS; -.
DR OrthoDB; 861683at2; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000001409; 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 3: Inferred from homology;
KW Amino-acid biosynthesis; Decarboxylase; Lyase; Lysine biosynthesis;
KW Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..459
FT /note="Diaminopimelate decarboxylase"
FT /id="PRO_0000149920"
FT ACT_SITE 388
FT /note="Proton donor"
FT /evidence="ECO:0000255"
FT BINDING 271
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 313..316
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 316
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 357
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 361
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 389
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 418
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 418
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT MOD_RES 89
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
SQ SEQUENCE 459 AA; 49015 MW; 8000ED54C7AB985B CRC64;
MTAETETGIP GVPGTQAADQ FNELPAHVWP RNAVRQEDGV VTVAGVPLPD LAEEYGTPLF
VVDEDDFRAR CRDMASAFGG PDRVHYASKA FLSKTVARWV DEEGLSLDIA SENELGIALA
ADFPGERITA HGNNKDASFL RACVRNNLGH VVLDSAQELE LLDYIAAGEG KVQPVLIRVK
PGIEAHTHEF IATSHEDQKF GFSLASGAAF DAARAAVNAE NLELVGLHCH VGSQVFDAQG
FSLAAERVLE LYSRIHDELG VTLAELDLGG GYGIAYTAAE EPLNVVEVAH DLLTAVGKTA
AELGIEAPTV LVEPGRAIAG PSTVTVYEVG TIKDVDVDDE TTRRYISVDG GMSDNIRPAL
YGAEYDARVV SRFTEGETTN TRVVGSHCES GDILINEATY PSDIHTGDLL ALAATGAYCY
AMSSRYNAFA RPAVVSVRAG AAKLMLRRET LDDILSLEV
