DCDA_CORGL
ID DCDA_CORGL Reviewed; 445 AA.
AC P09890; P41254;
DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1989, sequence version 1.
DT 03-AUG-2022, entry version 148.
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};
GN OrderedLocusNames=Cgl1180, cg1334;
OS Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 /
OS JCM 1318 / LMG 3730 / NCIMB 10025).
OC Bacteria; Actinobacteria; Corynebacteriales; Corynebacteriaceae;
OC Corynebacterium.
OX NCBI_TaxID=196627;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 13059 / LMG 3658 / NCIB 10332 / AS019 / 613;
RX PubMed=2836698; DOI=10.1007/bf00322452;
RA Yeh P., Sicard A.M., Sinskey A.J.;
RT "Nucleotide sequence of the lysA gene of Corynebacterium glutamicum and
RT possible mechanisms for modulation of its expression.";
RL Mol. Gen. Genet. 212:112-119(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025;
RX PubMed=12743753; DOI=10.1007/s00253-003-1328-1;
RA Ikeda M., Nakagawa S.;
RT "The Corynebacterium glutamicum genome: features and impacts on
RT biotechnological processes.";
RL Appl. Microbiol. Biotechnol. 62:99-109(2003).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025;
RX PubMed=12948626; DOI=10.1016/s0168-1656(03)00154-8;
RA Kalinowski J., Bathe B., Bartels D., Bischoff N., Bott M., Burkovski A.,
RA Dusch N., Eggeling L., Eikmanns B.J., Gaigalat L., Goesmann A.,
RA Hartmann M., Huthmacher K., Kraemer R., Linke B., McHardy A.C., Meyer F.,
RA Moeckel B., Pfefferle W., Puehler A., Rey D.A., Rueckert C., Rupp O.,
RA Sahm H., Wendisch V.F., Wiegraebe I., Tauch A.;
RT "The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its
RT impact on the production of L-aspartate-derived amino acids and vitamins.";
RL J. Biotechnol. 104:5-25(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-49, AND INDUCTION.
RC STRAIN=ATCC 13059 / LMG 3658 / NCIB 10332 / AS019 / 613;
RX PubMed=2082143; DOI=10.1111/j.1365-2958.1990.tb02030.x;
RA Marcel T., Archer J.A.C., Mengin-Lecreulx D., Sinskey A.J.;
RT "Nucleotide sequence and organization of the upstream region of the
RT Corynebacterium glutamicum lysA gene.";
RL Mol. Microbiol. 4:1819-1830(1990).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-49.
RC STRAIN=ATCC 13869 / DSMZ 1412 / NCIMB 9567;
RX PubMed=8226683; DOI=10.1128/jb.175.22.7356-7362.1993;
RA Oguiza J.A., Malumbres M., Eriani G., Pisabarro A., Mateos L.M., Martin F.,
RA Martin J.F.;
RT "A gene encoding arginyl-tRNA synthetase is located in the upstream region
RT of the lysA gene in Brevibacterium lactofermentum: regulation of argS-lysA
RT cluster expression by arginine.";
RL J. Bacteriol. 175:7356-7362(1993).
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 -!- INDUCTION: Up-regulated by arginine and repressed by lysine.
CC {ECO:0000269|PubMed:2082143}.
CC -!- MISCELLANEOUS: Both, substrate and product of the catalyzed reaction
CC are critical for cell growth.
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; X07563; CAA30445.1; -; Genomic_DNA.
DR EMBL; BA000036; BAB98573.1; -; Genomic_DNA.
DR EMBL; BX927151; CAF19884.1; -; Genomic_DNA.
DR EMBL; X54740; CAA38538.1; -; Genomic_DNA.
DR EMBL; Z21501; CAA79711.1; -; Genomic_DNA.
DR PIR; S03827; S03827.
DR RefSeq; NP_600406.1; NC_003450.3.
DR RefSeq; WP_011014180.1; NC_006958.1.
DR PDB; 5X7M; X-ray; 2.40 A; A/B=1-445.
DR PDB; 5X7N; X-ray; 1.72 A; A/B=1-445.
DR PDBsum; 5X7M; -.
DR PDBsum; 5X7N; -.
DR AlphaFoldDB; P09890; -.
DR SMR; P09890; -.
DR STRING; 196627.cg1334; -.
DR KEGG; cgb:cg1334; -.
DR KEGG; cgl:Cgl1180; -.
DR PATRIC; fig|196627.13.peg.1159; -.
DR eggNOG; COG0019; Bacteria.
DR HOGENOM; CLU_026444_0_1_11; -.
DR OMA; YCRSMAS; -.
DR BRENDA; 4.1.1.20; 960.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000000582; 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 3D-structure; Amino-acid biosynthesis; Decarboxylase; Lyase;
KW Lysine biosynthesis; Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..445
FT /note="Diaminopimelate decarboxylase"
FT /id="PRO_0000149921"
FT ACT_SITE 374
FT /note="Proton donor"
FT /evidence="ECO:0000255"
FT BINDING 257
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 299..302
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 302
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 343
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 347
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 375
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 404
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 404
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT MOD_RES 75
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT HELIX 4..7
FT /evidence="ECO:0007829|PDB:5X7N"
FT TURN 12..14
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 19..21
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 25..29
FT /evidence="ECO:0007829|PDB:5X7N"
FT HELIX 34..41
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 43..49
FT /evidence="ECO:0007829|PDB:5X7N"
FT HELIX 50..63
FT /evidence="ECO:0007829|PDB:5X7N"
FT HELIX 67..69
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 70..73
FT /evidence="ECO:0007829|PDB:5X7N"
FT HELIX 74..76
FT /evidence="ECO:0007829|PDB:5X7N"
FT HELIX 80..88
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 92..95
FT /evidence="ECO:0007829|PDB:5X7N"
FT HELIX 98..106
FT /evidence="ECO:0007829|PDB:5X7N"
FT HELIX 111..113
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 114..116
FT /evidence="ECO:0007829|PDB:5X7N"
FT HELIX 123..132
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 135..139
FT /evidence="ECO:0007829|PDB:5X7N"
FT HELIX 142..155
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 159..166
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 168..171
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 176..178
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 184..190
FT /evidence="ECO:0007829|PDB:5X7N"
FT HELIX 194..204
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 208..214
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 218..221
FT /evidence="ECO:0007829|PDB:5X7N"
FT HELIX 225..245
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 251..253
FT /evidence="ECO:0007829|PDB:5X7N"
FT HELIX 271..289
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 295..298
FT /evidence="ECO:0007829|PDB:5X7N"
FT HELIX 302..305
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 309..326
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 328..335
FT /evidence="ECO:0007829|PDB:5X7N"
FT TURN 338..340
FT /evidence="ECO:0007829|PDB:5X7N"
FT HELIX 343..347
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 353..358
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 364..370
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 372..375
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 379..387
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 395..399
FT /evidence="ECO:0007829|PDB:5X7N"
FT TURN 402..405
FT /evidence="ECO:0007829|PDB:5X7N"
FT HELIX 406..408
FT /evidence="ECO:0007829|PDB:5X7N"
FT HELIX 412..414
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 419..424
FT /evidence="ECO:0007829|PDB:5X7N"
FT STRAND 427..432
FT /evidence="ECO:0007829|PDB:5X7N"
FT HELIX 437..442
FT /evidence="ECO:0007829|PDB:5X7N"
SQ SEQUENCE 445 AA; 47411 MW; F7F49A23EAA6CAB3 CRC64;
MATVENFNEL PAHVWPRNAV RQEDGVVTVA GVPLPDLAEE YGTPLFVVDE DDFRSRCRDM
ATAFGGPGNV HYASKAFLTK TIARWVDEEG LALDIASINE LGIALAAGFP ASRITAHGNN
KGVEFLRALV QNGVGHVVLD SAQELELLDY VAAGEGKIQD VLIRVKPGIE AHTHEFIATS
HEDQKFGFSL ASGSAFEAAK AANNAENLNL VGLHCHVGSQ VFDAEGFKLA AERVLGLYSQ
IHSELGVALP ELDLGGGYGI AYTAAEEPLN VAEVASDLLT AVGKMAAELG IDAPTVLVEP
GRAIAGPSTV TIYEVGTTKD VHVDDDKTRR YIAVDGGMSD NIRPALYGSE YDARVVSRFA
EGDPVSTRIV GSHCESGDIL INDEIYPSDI TSGDFLALAA TGAYCYAMSS RYNAFTRPAV
VSVRAGSSRL MLRRETLDDI LSLEA
