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Database: UniProt
Entry: A0A037ZKL7_9RHOB
LinkDB: A0A037ZKL7_9RHOB
Original site: A0A037ZKL7_9RHOB 
ID   A0A037ZKL7_9RHOB        Unreviewed;       421 AA.
AC   A0A037ZKL7;
DT   09-JUL-2014, integrated into UniProtKB/TrEMBL.
DT   09-JUL-2014, sequence version 1.
DT   24-JAN-2024, entry version 42.
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   ORFNames=ACMU_10085 {ECO:0000313|EMBL:KAJ56097.1};
OS   Actibacterium mucosum KCTC 23349.
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales;
OC   Roseobacteraceae; Actibacterium.
OX   NCBI_TaxID=1454373 {ECO:0000313|EMBL:KAJ56097.1, ECO:0000313|Proteomes:UP000026249};
RN   [1] {ECO:0000313|EMBL:KAJ56097.1, ECO:0000313|Proteomes:UP000026249}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=KCTC 23349 {ECO:0000313|EMBL:KAJ56097.1,
RC   ECO:0000313|Proteomes:UP000026249};
RA   Arahal D.R., Shao Z., Lai Q., Pujalte M.J.;
RT   "Draft Genome Sequence of Actibacterium mucosum KCTC 23349, a Marine
RT   Alphaproteobacterium with Complex Ionic Requirements Isolated from
RT   Mediterranean Seawater at Malvarrosa Beach, Valencia, Spain.";
RL   Submitted (MAR-2014) 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}.
CC   -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC       whole genome shotgun (WGS) entry which is preliminary data.
CC       {ECO:0000313|EMBL:KAJ56097.1}.
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DR   EMBL; JFKE01000003; KAJ56097.1; -; Genomic_DNA.
DR   RefSeq; WP_035258292.1; NZ_JFKE01000003.1.
DR   AlphaFoldDB; A0A037ZKL7; -.
DR   STRING; 1454373.ACMU_10085; -.
DR   OrthoDB; 9802241at2; -.
DR   UniPathway; UPA00034; UER00027.
DR   Proteomes; UP000026249; Unassembled WGS sequence.
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:UP000026249}.
FT   DOMAIN          36..281
FT                   /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT                   /evidence="ECO:0000259|Pfam:PF02784"
FT   DOMAIN          282..373
FT                   /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT                   /evidence="ECO:0000259|Pfam:PF00278"
FT   ACT_SITE        346
FT                   /note="Proton donor"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR600183-50"
FT   BINDING         239
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         347
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   BINDING         375
FT                   /ligand="pyridoxal 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:597326"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   BINDING         375
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT   MOD_RES         60
FT                   /note="N6-(pyridoxal phosphate)lysine"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_02120,
FT                   ECO:0000256|PIRSR:PIRSR600183-50"
SQ   SEQUENCE   421 AA;  45600 MW;  70CFA25A1C3472D5 CRC64;
     MDHFLYRDGI LHAEDVPLSQ IAAAVGTPFY CYSTATFTRH FRLFDEALEG MPHLVCYAMK
     ANSNQAILTL MANLGAGVDV VSGGEYARAR AAGFEGDKIV FSGVGKTRDE MRTALAGGIR
     QFNLESEPEM RVLDQVARAM GVVAPVTVRV NPDVDAKTHE KIATGKSENK FGIPIAKARE
     VYAEIATLEG LRVVGIDVHI GSQLTDLEPY RLAYRKVAEL TDVLRADGHA IERLDLGGGL
     GIPYERSNDA PPLPVEYGAM VREELGHLNA EIEIEPGRLI AGNSGVLVTE VIYLKEGEGR
     DFLIVDAAMN DLIRPSMYAA HHDIVSVVEP AAGADPATYD VVGPVCESGD TFAKQRVMAQ
     SGPGDLIAFR SAGAYGAVMA SEYNSRPLVP EVLVSGDQFA VIRPRPSFDE MINRDRVPEW
     L
//
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