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Database: UniProt
Entry: Q32C83_SHIDS
LinkDB: Q32C83_SHIDS
Original site: Q32C83_SHIDS 
ID   Q32C83_SHIDS            Unreviewed;       420 AA.
AC   Q32C83;
DT   06-DEC-2005, integrated into UniProtKB/TrEMBL.
DT   06-DEC-2005, sequence version 1.
DT   24-JAN-2024, entry version 117.
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   ECO:0000313|EMBL:ABB63072.1};
GN   OrderedLocusNames=SDY_3055 {ECO:0000313|EMBL:ABB63072.1};
OS   Shigella dysenteriae serotype 1 (strain Sd197).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Shigella.
OX   NCBI_TaxID=300267 {ECO:0000313|EMBL:ABB63072.1, ECO:0000313|Proteomes:UP000002716};
RN   [1] {ECO:0000313|EMBL:ABB63072.1, ECO:0000313|Proteomes:UP000002716}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Sd197 {ECO:0000313|EMBL:ABB63072.1,
RC   ECO:0000313|Proteomes:UP000002716};
RX   PubMed=16275786; DOI=10.1093/nar/gki954;
RA   Yang F., Yang J., Zhang X., Chen L., Jiang Y., Yan Y., Tang X., Wang J.,
RA   Xiong Z., Dong J., Xue Y., Zhu Y., Xu X., Sun L., Chen S., Nie H., Peng J.,
RA   Xu J., Wang Y., Yuan Z., Wen Y., Yao Z., Shen Y., Qiang B., Hou Y., Yu J.,
RA   Jin Q.;
RT   "Genome dynamics and diversity of Shigella species, the etiologic agents of
RT   bacillary dysentery.";
RL   Nucleic Acids Res. 33:6445-6458(2005).
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,
CC         ECO:0000256|HAMAP-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}.
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DR   EMBL; CP000034; ABB63072.1; -; Genomic_DNA.
DR   RefSeq; WP_001120691.1; NC_007606.1.
DR   RefSeq; YP_404563.1; NC_007606.1.
DR   AlphaFoldDB; Q32C83; -.
DR   STRING; 300267.SDY_3055; -.
DR   EnsemblBacteria; ABB63072; ABB63072; SDY_3055.
DR   KEGG; sdy:SDY_3055; -.
DR   PATRIC; fig|300267.13.peg.3660; -.
DR   HOGENOM; CLU_026444_0_2_6; -.
DR   OMA; HGNAKSP; -.
DR   UniPathway; UPA00034; UER00027.
DR   Proteomes; UP000002716; 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; 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   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.
DR   PROSITE; PS00879; ODR_DC_2_2; 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:UP000002716}.
FT   DOMAIN          33..275
FT                   /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT                   /evidence="ECO:0000259|Pfam:PF02784"
FT   DOMAIN          276..376
FT                   /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT                   /evidence="ECO:0000259|Pfam:PF00278"
FT   ACT_SITE        342
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         268..271
FT                   /ligand="pyridoxal 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:597326"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   BINDING         271
FT                   /ligand="substrate"
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         343
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   BINDING         378
FT                   /ligand="pyridoxal 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:597326"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   BINDING         378
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   MOD_RES         54
FT                   /note="N6-(pyridoxal phosphate)lysine"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120,
FT                   ECO:0000256|PIRSR:PIRSR600183-50"
SQ   SEQUENCE   420 AA;  46162 MW;  15143F07800E8674 CRC64;
     MPHSLFSTDT ALTAENLLRL PAEFGCPVWV YDAQIIRRQI AALKQFDVVR FAQKACSNIH
     ILRLMREQGV KVDSVSLGEI ERALAAGYNP QTHPDDIVFT ADVIDQATLE RVSELQIPVN
     AGSVDMLDQL GQVSPGHRVW LRVNPGFGHG HSQKTNTGGE NSKHGIWYTD LPAALDVIQR
     HHLQLVGIHM HIGSGVDYAH LEQVCGAMVR QVIEFGQDLQ AISAGGGLSI PYQQGEEAVD
     TEHYYGLWNA ARQQIARHLG HPVKLEIEPG RFLVAQSGVL ITQVRSVKQM GSRHFVLVDA
     GFNDLMRPAM YGSYHHISAL AADGRSLEHA PTVETVVAGP LCESGDVFTQ QEGGNVETRA
     LLEVKAGDYL VLHDTGAYGA SMSSNYNSRP LLPEVLFDNG QARLIRRRQT IEELLALELL
//
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