ID   A0A0H2VXI6_SHIFL        Unreviewed;       420 AA.
AC   A0A0H2VXI6; A0A2G3FRL7; Q7C059; Q83QB7;
DT   23-MAY-2018, integrated into UniProtKB/TrEMBL.
DT   23-MAY-2018, sequence version 1.
DT   24-JAN-2024, entry version 30.
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:AAN44334.1};
GN   OrderedLocusNames=SF2848 {ECO:0000313|EMBL:AAN44334.1};
OS   Shigella flexneri.
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Shigella.
OX   NCBI_TaxID=623 {ECO:0000313|EMBL:AAN44334.1, ECO:0000313|Proteomes:UP000001006};
RN   [1] {ECO:0000313|EMBL:AAN44334.1, ECO:0000313|Proteomes:UP000001006}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=301 / Serotype 2a {ECO:0000313|Proteomes:UP000001006};
RX   PubMed=12384590; DOI=10.1093/nar/gkf566;
RA   Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H., Yang J.,
RA   Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J., Sun L.,
RA   Xue Y., Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S., Cheng H.,
RA   Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou Y., Yu J.;
RT   "Genome sequence of Shigella flexneri 2a: insights into pathogenicity
RT   through comparison with genomes of Escherichia coli K12 and O157.";
RL   Nucleic Acids Res. 30:4432-4441(2002).
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}.
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DR   EMBL; AE005674; AAN44334.1; -; Genomic_DNA.
DR   RefSeq; NP_708627.1; NC_004337.2.
DR   RefSeq; WP_001120740.1; NZ_WPGW01000008.1.
DR   AlphaFoldDB; A0A0H2VXI6; -.
DR   PaxDb; 198214-SF2848; -.
DR   GeneID; 1025821; -.
DR   KEGG; sfl:SF2848; -.
DR   PATRIC; fig|198214.7.peg.3389; -.
DR   OMA; HGNAKSP; -.
DR   UniPathway; UPA00034; UER00027.
DR   Proteomes; UP000001006; 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:UP000001006}.
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;  46175 MW;  5CF953BC40B338F9 CRC64;
     MPHSLFSTDT DLTAENLLRL PAEFGCPVWV YDAQIIRRQI AALKQFEVVR FAQKACSNIH
     ILRLMREQGV KVDSVSLGEI ERALAAGYNP QTHPDDIVFT ADVIDQATLE RVSELQIPVN
     AGSVDTLDQL GQVSPGHRVW LRVNPGFGHG HSQKTNTGGE NSKHGIWYTD LPAALDVIQR
     HHLQLVGIHM HIGSGVDYAH LEQVCGAMVR QVIEFGQDLQ AISAGGGLSI PYQQGEEAVD
     TEHYYGLWNA AREQIARHLG HPVKLEIEPG RFLVAQSGVL ITQVRSVKQM GSRHFVLVDA
     GFNDLMRPAM YGSYHHISAL AADGRSLEHA PTVETVVAGP LCESGDVFTQ QEGGNVETRA
     LPEVKAGDYL VLHDTGAYGA SMSSNYNSRP LLPEVLFDNG QARLIRRRQT IEELLALELL
//