ID   G0IVQ1_CYCMS            Unreviewed;       410 AA.
AC   G0IVQ1;
DT   19-OCT-2011, integrated into UniProtKB/TrEMBL.
DT   19-OCT-2011, sequence version 1.
DT   27-MAR-2024, entry version 68.
DE   RecName: Full=Diaminopimelate decarboxylase {ECO:0000256|HAMAP-Rule:MF_02120, ECO:0000256|RuleBase:RU003738};
DE            Short=DAP decarboxylase {ECO:0000256|HAMAP-Rule:MF_02120};
DE            Short=DAPDC {ECO:0000256|HAMAP-Rule:MF_02120};
DE            EC=4.1.1.20 {ECO:0000256|HAMAP-Rule:MF_02120, ECO:0000256|RuleBase:RU003738};
GN   Name=lysA {ECO:0000256|HAMAP-Rule:MF_02120};
GN   OrderedLocusNames=Cycma_1046 {ECO:0000313|EMBL:AEL24818.1};
OS   Cyclobacterium marinum (strain ATCC 25205 / DSM 745 / LMG 13164 / NCIMB
OS   1802) (Flectobacillus marinus).
OC   Bacteria; Bacteroidota; Cytophagia; Cytophagales; Cyclobacteriaceae;
OC   Cyclobacterium.
OX   NCBI_TaxID=880070 {ECO:0000313|EMBL:AEL24818.1, ECO:0000313|Proteomes:UP000001635};
RN   [1] {ECO:0000313|Proteomes:UP000001635}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 25205 / DSM 745 / LMG 13164 / NCIMB 1802
RC   {ECO:0000313|Proteomes:UP000001635};
RA   Lucas S., Han J., Lapidus A., Bruce D., Goodwin L., Pitluck S., Peters L.,
RA   Kyrpides N., Mavromatis K., Ivanova N., Ovchinnikova G., Chertkov O.,
RA   Detter J.C., Tapia R., Han C., Land M., Hauser L., Markowitz V.,
RA   Cheng J.-F., Hugenholtz P., Woyke T., Wu D., Tindall B., Schuetze A.,
RA   Brambilla E., Klenk H.-P., Eisen J.A.;
RT   "The complete genome of Cyclobacterium marinum DSM 745.";
RL   Submitted (JUL-2011) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: Specifically catalyzes the decarboxylation of meso-
CC       diaminopimelate (meso-DAP) to L-lysine. {ECO:0000256|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:0000256|HAMAP-Rule:MF_02120,
CC         ECO:0000256|RuleBase:RU003738};
CC   -!- COFACTOR:
CC       Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC         Evidence={ECO:0000256|ARBA:ARBA00001933, ECO:0000256|HAMAP-
CC         Rule:MF_02120, ECO:0000256|PIRSR:PIRSR600183-50,
CC         ECO:0000256|RuleBase:RU003738};
CC   -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC       pathway; L-lysine from DL-2,6-diaminopimelate: step 1/1.
CC       {ECO:0000256|HAMAP-Rule:MF_02120, ECO:0000256|RuleBase:RU003738}.
CC   -!- SUBUNIT: Homodimer. {ECO:0000256|HAMAP-Rule:MF_02120}.
CC   -!- SIMILARITY: Belongs to the Orn/Lys/Arg decarboxylase class-II family.
CC       LysA subfamily. {ECO:0000256|HAMAP-Rule:MF_02120}.
CC   -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC       feature annotation. {ECO:0000256|HAMAP-Rule:MF_02120}.
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DR   EMBL; CP002955; AEL24818.1; -; Genomic_DNA.
DR   RefSeq; WP_014019115.1; NC_015914.1.
DR   AlphaFoldDB; G0IVQ1; -.
DR   STRING; 880070.Cycma_1046; -.
DR   KEGG; cmr:Cycma_1046; -.
DR   eggNOG; COG0019; Bacteria.
DR   HOGENOM; CLU_026444_0_2_10; -.
DR   OrthoDB; 9802241at2; -.
DR   UniPathway; UPA00034; UER00027.
DR   Proteomes; UP000001635; 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; 3.20.20.10; Alanine racemase; 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; 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   NCBIfam; TIGR01048; lysA; 1.
DR   PANTHER; PTHR43727; DIAMINOPIMELATE DECARBOXYLASE; 1.
DR   PANTHER; PTHR43727:SF2; DIAMINOPIMELATE DECARBOXYLASE 1, CHLOROPLASTIC-RELATED; 1.
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; Alanine racemase C-terminal domain-like; 1.
DR   SUPFAM; SSF51419; PLP-binding barrel; 1.
DR   PROSITE; PS00878; ODR_DC_2_1; 1.
PE   3: Inferred from homology;
KW   Amino-acid biosynthesis {ECO:0000256|HAMAP-Rule:MF_02120};
KW   Decarboxylase {ECO:0000256|HAMAP-Rule:MF_02120,
KW   ECO:0000256|RuleBase:RU003738};
KW   Lyase {ECO:0000256|HAMAP-Rule:MF_02120, ECO:0000256|RuleBase:RU003738};
KW   Lysine biosynthesis {ECO:0000256|HAMAP-Rule:MF_02120,
KW   ECO:0000256|RuleBase:RU003738};
KW   Pyridoxal phosphate {ECO:0000256|HAMAP-Rule:MF_02120,
KW   ECO:0000256|PIRSR:PIRSR600183-50};
KW   Reference proteome {ECO:0000313|Proteomes:UP000001635}.
FT   DOMAIN          33..275
FT                   /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT                   /evidence="ECO:0000259|Pfam:PF02784"
FT   DOMAIN          276..363
FT                   /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT                   /evidence="ECO:0000259|Pfam:PF00278"
FT   ACT_SITE        337
FT                   /note="Proton donor"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR600183-50"
FT   BINDING         227
FT                   /ligand="pyridoxal 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:597326"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   BINDING         307
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   BINDING         311
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   BINDING         338
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   BINDING         365
FT                   /ligand="pyridoxal 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:597326"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   BINDING         365
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   MOD_RES         57
FT                   /note="N6-(pyridoxal phosphate)lysine"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120,
FT                   ECO:0000256|PIRSR:PIRSR600183-50"
SQ   SEQUENCE   410 AA;  45651 MW;  0E0AC58257A72972 CRC64;
     MEIKNQQYCI GGIPLLNIAE KYGSPVYVYD GEKILHQVES LKKAFADVKM KIKYATKALS
     NINILKLMKK AGTGVDAVSI EEVKLCLHVG FSPEEIMYTP NCVDFEEIKE AVAYGVMVNI
     DSIPMLEHFG TEYGNDVPIC IRLNPHILAG GNAKISVGHI DSKFGISILQ LKHVIKVVQA
     YDLNVVGLHV HTGSDILDAE VFLQGAEILF DAAREFKDLA FLDFGGGFKV AYKNGDITTD
     IQDVGKKVSA AFKKFCKEYG RELEIWFEPG KFLVSECGYL LTKANVVKPT PATTFVGVNS
     GLNHLLRPMM YDAYHSVVNI SKLDGPERVY TIVGYICETD TIAADRKIKE VKEGDIIAIK
     NAGAYGYSMS SNYNSRFRPA EVLILNEKDY LIRKRESMED ILKNQISIDF
//