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Entry: A0A1S1NR42_9GAMM
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ID   A0A1S1NR42_9GAMM        Unreviewed;       422 AA.
AC   A0A1S1NR42;
DT   12-APR-2017, integrated into UniProtKB/TrEMBL.
DT   12-APR-2017, sequence version 1.
DT   24-JAN-2024, entry version 27.
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:QEL09800.1};
GN   ORFNames=BH688_13765 {ECO:0000313|EMBL:OHV08377.1}, FY550_00740
GN   {ECO:0000313|EMBL:QEL09800.1};
OS   Kushneria phosphatilytica.
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Oceanospirillales;
OC   Halomonadaceae; Kushneria.
OX   NCBI_TaxID=657387 {ECO:0000313|EMBL:OHV08377.1, ECO:0000313|Proteomes:UP000179907};
RN   [1] {ECO:0000313|EMBL:OHV08377.1, ECO:0000313|Proteomes:UP000179907}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=YCWA18 {ECO:0000313|EMBL:OHV08377.1,
RC   ECO:0000313|Proteomes:UP000179907};
RA   Wang C., Qu L.;
RT   "The draft genome suquence of Kushneria sp. YCWA18.";
RL   Submitted (OCT-2016) to the EMBL/GenBank/DDBJ databases.
RN   [2] {ECO:0000313|EMBL:QEL09800.1, ECO:0000313|Proteomes:UP000322553}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=YCWA18 {ECO:0000313|EMBL:QEL09800.1,
RC   ECO:0000313|Proteomes:UP000322553};
RA   Du G.-X., Qu L.-Y.;
RT   "Complete genome sequence of Kushneria sp. YCWA18, a halophilic phosphate-
RT   solubilizing bacterium isolated from Daqiao saltern in China.";
RL   Submitted (AUG-2019) 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,
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; MKZT01000020; OHV08377.1; -; Genomic_DNA.
DR   EMBL; CP043420; QEL09800.1; -; Genomic_DNA.
DR   RefSeq; WP_070980638.1; NZ_MKZT01000020.1.
DR   AlphaFoldDB; A0A1S1NR42; -.
DR   STRING; 657387.BH688_13765; -.
DR   KEGG; kuy:FY550_00740; -.
DR   OrthoDB; 9802241at2; -.
DR   UniPathway; UPA00034; UER00027.
DR   Proteomes; UP000179907; Unassembled WGS sequence.
DR   Proteomes; UP000322553; 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:UP000179907}.
FT   DOMAIN          38..282
FT                   /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT                   /evidence="ECO:0000259|Pfam:PF02784"
FT   DOMAIN          283..371
FT                   /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT                   /evidence="ECO:0000259|Pfam:PF00278"
FT   ACT_SITE        345
FT                   /note="Proton donor"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR600183-50"
FT   BINDING         241
FT                   /ligand="pyridoxal 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:597326"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   BINDING         275..278
FT                   /ligand="pyridoxal 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:597326"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   BINDING         278
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   BINDING         314
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   BINDING         318
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   BINDING         346
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   BINDING         373
FT                   /ligand="pyridoxal 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:597326"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   BINDING         373
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   MOD_RES         62
FT                   /note="N6-(pyridoxal phosphate)lysine"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120,
FT                   ECO:0000256|PIRSR:PIRSR600183-50"
SQ   SEQUENCE   422 AA;  45813 MW;  4AF319D8BD4B0340 CRC64;
     MTSPHFVYRQ GELYAEDAPL TRVAAQVGTP CYVYSKAAFT EHYRAYAQAL AGGPHLVCYA
     LKANSNLAVL GLLASLGAGF DIVSVGELER VLAVGGDPGR IVFSGVGKRE DEMRRALAVD
     IKCFNVESEA ELEQLARTAR SMGRTARVSL RVNPDVDAGT HPYISTGLKE NKFGIAIADA
     ERVYHYAREL AGVEPIGIDC HIGSQLTELS PFMDALDRLL ELHDRLAAAG IVIRHLDLGG
     GLGVDYQGET PPSPGEYIAA LRQRIGERPL ELILEPGRSI AANAGLMLTR VMYLKPGEHR
     SFAIVDGAMN DLIRPSLYQA WQRITAVCER HDVETHRWEI VGPVCESGDY LGHDRPLAIA
     AGDLLAVHSA GAYGFVMASN YNTRPRPPEV MIDGSEIHVV RQRERLDALW AGESLLPGAT
     PA
//
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