DCDA_VIBCH
ID DCDA_VIBCH Reviewed; 417 AA.
AC Q9KVL7;
DT 21-FEB-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=Diaminopimelate decarboxylase;
DE Short=DAP decarboxylase;
DE Short=DAPDC;
DE EC=4.1.1.20;
GN Name=lysA; OrderedLocusNames=VC_0125;
OS Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=243277;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 39315 / El Tor Inaba N16961;
RX PubMed=10952301; DOI=10.1038/35020000;
RA Heidelberg J.F., Eisen J.A., Nelson W.C., Clayton R.A., Gwinn M.L.,
RA Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L.A., Gill S.R.,
RA Nelson K.E., Read T.D., Tettelin H., Richardson D.L., Ermolaeva M.D.,
RA Vamathevan J.J., Bass S., Qin H., Dragoi I., Sellers P., McDonald L.A.,
RA Utterback T.R., Fleischmann R.D., Nierman W.C., White O., Salzberg S.L.,
RA Smith H.O., Colwell R.R., Mekalanos J.J., Venter J.C., Fraser C.M.;
RT "DNA sequence of both chromosomes of the cholera pathogen Vibrio
RT cholerae.";
RL Nature 406:477-483(2000).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS), AND SUBUNIT.
RG Center for Structural Genomics of Infectious Diseases (CSGID);
RT "1.8 Angstrom resolution crystal structure of diaminopimelate decarboxylase
RT (lysA) from Vibrio cholerae.";
RL Submitted (JUN-2010) to the PDB data bank.
CC -!- FUNCTION: Specifically catalyzes the decarboxylation of meso-
CC diaminopimelate (meso-DAP) to L-lysine. {ECO:0000250}.
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 -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000250};
CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC pathway; L-lysine from DL-2,6-diaminopimelate: step 1/1.
CC -!- SUBUNIT: Homodimer. {ECO:0000305|Ref.2}.
CC -!- SIMILARITY: Belongs to the Orn/Lys/Arg decarboxylase class-II family.
CC LysA subfamily. {ECO:0000305}.
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DR EMBL; AE003852; AAF93302.1; -; Genomic_DNA.
DR PIR; F82360; F82360.
DR RefSeq; NP_229783.1; NC_002505.1.
DR RefSeq; WP_000384387.1; NZ_LT906614.1.
DR PDB; 3N2B; X-ray; 1.80 A; A/B/C/D=1-417.
DR PDBsum; 3N2B; -.
DR AlphaFoldDB; Q9KVL7; -.
DR SMR; Q9KVL7; -.
DR STRING; 243277.VC_0125; -.
DR PRIDE; Q9KVL7; -.
DR DNASU; 2615366; -.
DR EnsemblBacteria; AAF93302; AAF93302; VC_0125.
DR GeneID; 57741378; -.
DR GeneID; 66940271; -.
DR KEGG; vch:VC_0125; -.
DR PATRIC; fig|243277.26.peg.116; -.
DR eggNOG; COG0019; Bacteria.
DR HOGENOM; CLU_026444_0_0_6; -.
DR OMA; YCRSMAS; -.
DR BioCyc; VCHO:VC0125-MON; -.
DR BRENDA; 4.1.1.20; 15862.
DR UniPathway; UPA00034; UER00027.
DR EvolutionaryTrace; Q9KVL7; -.
DR Proteomes; UP000000584; Chromosome 1.
DR GO; GO:0008836; F:diaminopimelate decarboxylase activity; IBA:GO_Central.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IBA:GO_Central.
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..417
FT /note="Diaminopimelate decarboxylase"
FT /id="PRO_0000149938"
FT ACT_SITE 344
FT /note="Proton donor"
FT /evidence="ECO:0000255"
FT BINDING 240
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT BINDING 275..278
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT BINDING 278
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 314
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 318
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 345
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 372
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT BINDING 372
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT MOD_RES 61
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250"
FT STRAND 3..6
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 10..14
FT /evidence="ECO:0007829|PDB:3N2B"
FT HELIX 19..26
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 28..34
FT /evidence="ECO:0007829|PDB:3N2B"
FT HELIX 35..48
FT /evidence="ECO:0007829|PDB:3N2B"
FT TURN 49..51
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 54..59
FT /evidence="ECO:0007829|PDB:3N2B"
FT HELIX 60..62
FT /evidence="ECO:0007829|PDB:3N2B"
FT HELIX 66..74
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 78..83
FT /evidence="ECO:0007829|PDB:3N2B"
FT HELIX 84..92
FT /evidence="ECO:0007829|PDB:3N2B"
FT HELIX 97..99
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 100..102
FT /evidence="ECO:0007829|PDB:3N2B"
FT HELIX 109..117
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 121..125
FT /evidence="ECO:0007829|PDB:3N2B"
FT HELIX 128..141
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 145..151
FT /evidence="ECO:0007829|PDB:3N2B"
FT TURN 157..159
FT /evidence="ECO:0007829|PDB:3N2B"
FT HELIX 161..168
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 170..174
FT /evidence="ECO:0007829|PDB:3N2B"
FT HELIX 176..178
FT /evidence="ECO:0007829|PDB:3N2B"
FT HELIX 179..188
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 192..198
FT /evidence="ECO:0007829|PDB:3N2B"
FT HELIX 208..227
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 234..236
FT /evidence="ECO:0007829|PDB:3N2B"
FT HELIX 255..264
FT /evidence="ECO:0007829|PDB:3N2B"
FT TURN 265..267
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 270..274
FT /evidence="ECO:0007829|PDB:3N2B"
FT HELIX 278..281
FT /evidence="ECO:0007829|PDB:3N2B"
FT HELIX 282..284
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 285..296
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 301..306
FT /evidence="ECO:0007829|PDB:3N2B"
FT TURN 309..311
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 324..328
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 335..340
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 342..345
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 349..356
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 363..368
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 370..373
FT /evidence="ECO:0007829|PDB:3N2B"
FT HELIX 374..376
FT /evidence="ECO:0007829|PDB:3N2B"
FT TURN 380..382
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 387..392
FT /evidence="ECO:0007829|PDB:3N2B"
FT STRAND 395..400
FT /evidence="ECO:0007829|PDB:3N2B"
FT HELIX 405..409
FT /evidence="ECO:0007829|PDB:3N2B"
SQ SEQUENCE 417 AA; 46277 MW; 17BD33D7E4C0836D CRC64;
MDYFNYQEDG QLWAEQVPLA DLANQYGTPL YVYSRATLER HWHAFDKSVG DYPHLICYAV
KANSNLGVLN TLARLGSGFD IVSVGELERV LAAGGDPSKV VFSGVGKTEA EMKRALQLKI
KCFNVESEPE LQRLNKVAGE LGVKAPISLR INPDVDAKTH PYISTGLRDN KFGITFDRAA
QVYRLAHSLP NLDVHGIDCH IGSQLTALAP FIDATDRLLA LIDSLKAEGI HIRHLDVGGG
LGVVYRDELP PQPSEYAKAL LDRLERHRDL ELIFEPGRAI AANAGVLVTK VEFLKHTEHK
NFAIIDAAMN DLIRPALYQA WQDIIPLRPR QGEAQTYDLV GPVCETSDFL GKDRDLVLQE
GDLLAVRSSG AYGFTMSSNY NTRPRVAEVM VDGNKTYLVR QREELSSLWA LESVLPE
