DCDA_BACSU
ID DCDA_BACSU Reviewed; 439 AA.
AC P23630;
DT 01-NOV-1991, integrated into UniProtKB/Swiss-Prot.
DT 14-APR-2009, sequence version 5.
DT 03-AUG-2022, entry version 155.
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}; Synonyms=lys;
GN OrderedLocusNames=BSU23380;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP PRELIMINARY NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2513554; DOI=10.1093/nar/17.23.10105;
RA Yamamoto J., Shimizu M., Yamane K.;
RT "Nucleotide sequence of the diaminopimelate-decarboxylase gene from
RT Bacillus subtilis.";
RL Nucleic Acids Res. 17:10105-10105(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB
RC 3610 / NRRL NRS-744 / VKM B-501;
RX PubMed=7934829; DOI=10.1111/j.1365-2958.1993.tb02670.x;
RA Sorokin A.V., Zumstein E., Azevedo V., Ehrlich S.D., Serror P.;
RT "The organization of the Bacillus subtilis 168 chromosome region between
RT the spoVA and serA genetic loci, based on sequence data.";
RL Mol. Microbiol. 10:385-395(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1368705; DOI=10.1271/bbb1961.55.1615;
RA Yamamoto J., Shimizu M., Yamane K.;
RT "Molecular cloning and analysis of nucleotide sequence of the Bacillus
RT subtilis lysA gene region using B. subtilis phage vectors and a multi-copy
RT plasmid, pUB110.";
RL Agric. Biol. Chem. 55:1615-1626(1991).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / JH642;
RX PubMed=8969508; DOI=10.1099/13500872-142-11-3103;
RA Mizuno M., Masuda S., Takemaru K., Hosono S., Sato T., Takeuchi M.,
RA Kobayashi Y.;
RT "Systematic sequencing of the 283 kb 210 degrees-232 degrees region of the
RT Bacillus subtilis genome containing the skin element and many sporulation
RT genes.";
RL Microbiology 142:3103-3111(1996).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA12662.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=BAA14211.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; X17013; CAA34876.1; ALT_SEQ; Genomic_DNA.
DR EMBL; L09228; AAA67473.1; -; Genomic_DNA.
DR EMBL; D90189; BAA14211.1; ALT_INIT; Genomic_DNA.
DR EMBL; D84432; BAA12662.1; ALT_INIT; Genomic_DNA.
DR EMBL; AL009126; CAB14270.1; -; Genomic_DNA.
DR PIR; S45535; JU0471.
DR RefSeq; NP_390219.1; NC_000964.3.
DR RefSeq; WP_004398851.1; NZ_JNCM01000036.1.
DR AlphaFoldDB; P23630; -.
DR SMR; P23630; -.
DR STRING; 224308.BSU23380; -.
DR PaxDb; P23630; -.
DR PRIDE; P23630; -.
DR EnsemblBacteria; CAB14270; CAB14270; BSU_23380.
DR GeneID; 938931; -.
DR KEGG; bsu:BSU23380; -.
DR PATRIC; fig|224308.179.peg.2547; -.
DR eggNOG; COG0019; Bacteria.
DR InParanoid; P23630; -.
DR OMA; YCRSMAS; -.
DR PhylomeDB; P23630; -.
DR BioCyc; BSUB:BSU23380-MON; -.
DR BioCyc; MetaCyc:MON-6601; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000001570; Chromosome.
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 3: Inferred from homology;
KW Amino-acid biosynthesis; Decarboxylase; Lyase; Lysine biosynthesis;
KW Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..439
FT /note="Diaminopimelate decarboxylase"
FT /id="PRO_0000149915"
FT ACT_SITE 361
FT /note="Proton donor"
FT /evidence="ECO:0000255"
FT BINDING 248
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 290..293
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 293
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 330
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 334
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 362
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 390
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 390
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT MOD_RES 66
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT CONFLICT 90..137
FT /note="GELYTAVAAGFPAERIHFHGNNKSREELRMALEHRIGCIVVDNFYEIA ->
FT ESYIRLLQQAFRQNASTFMETIRAGKNCGWRLSTASAALWWIISMKSS (in Ref.
FT 3; BAA14211)"
FT /evidence="ECO:0000305"
FT CONFLICT 159
FT /note="G -> R (in Ref. 3; BAA14211)"
FT /evidence="ECO:0000305"
FT CONFLICT 385..388
FT /note="FCTG -> LYR (in Ref. 3; BAA14211)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 439 AA; 48574 MW; 5AE8DEACFE43BB30 CRC64;
MFLHGTSRQN QHGHLEIGGV DALYLAEKYG TPLYVYDVAL IRERAKSFKQ AFISAGLKAQ
VAYASKAFSS VAMIQLAEEE GLSLDVVSGG ELYTAVAAGF PAERIHFHGN NKSREELRMA
LEHRIGCIVV DNFYEIALLE DLCKETGHSI DVLLRITPGV EAHTHDYITT GQEDSKFGFD
LHNGQTERAI EQVLQSEHIQ LLGVHCHIGS QIFDTAGFVL AAEKIFKKLD EWRDSYSFVS
KVLNLGGGFG IRYTEDDEPL HATEYVEKII EAVKENASRY GFDIPEIWIE PGRSLVGDAG
TTLYTVGSQK EVPGVRQYVA VDGGMNDNIR PALYQAKYEA AAANRIGEAH DKTVSIAGKC
CESGDMLIWD IDLPEVKEGD LLAVFCTGAY GYSMANNYNR IPRPAVVFVE NGEAHLVVKR
ETYEDIVKLD LPFKTGVKQ
