(data stored in SCRATCH zone)

SWISSPROT: 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   11-DEC-2019, entry version 145.
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 / 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-diaminopimelate = 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};
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   SMR; P23630; -.
DR   STRING; 224308.BSU23380; -.
DR   PaxDb; P23630; -.
DR   PRIDE; P23630; -.
DR   EnsemblBacteria; CAB14270; CAB14270; BSU23380.
DR   GeneID; 938931; -.
DR   KEGG; bsu:BSU23380; -.
DR   PATRIC; fig|224308.179.peg.2547; -.
DR   eggNOG; ENOG4105CU5; Bacteria.
DR   eggNOG; COG0019; LUCA.
DR   HOGENOM; HOG000045071; -.
DR   InParanoid; P23630; -.
DR   KO; K01586; -.
DR   OMA; VVGYICE; -.
DR   PhylomeDB; P23630; -.
DR   BioCyc; BSUB:BSU23380-MONOMER; -.
DR   BioCyc; MetaCyc:MONOMER-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;
DR   PRODOM; P23630.
DR   SWISS-2DPAGE; P23630.
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   REGION          290..293
FT                   /note="Pyridoxal phosphate binding"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT   ACT_SITE        361
FT                   /note="Proton donor"
FT                   /evidence="ECO:0000255"
FT   BINDING         248
FT                   /note="Pyridoxal phosphate; via amide nitrogen"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT   BINDING         293
FT                   /note="Substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT   BINDING         330
FT                   /note="Substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT   BINDING         334
FT                   /note="Substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT   BINDING         362
FT                   /note="Substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT   BINDING         390
FT                   /note="Pyridoxal phosphate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT   BINDING         390
FT                   /note="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
//

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