ID V4PKH1_9CAUL Unreviewed; 438 AA.
AC V4PKH1;
DT 22-JAN-2014, integrated into UniProtKB/TrEMBL.
DT 22-JAN-2014, sequence version 1.
DT 24-JAN-2024, entry version 48.
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=AEAC466_01800 {ECO:0000313|EMBL:ESQ85940.1};
OS Asticcacaulis sp. AC466.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Caulobacterales;
OC Caulobacteraceae; Asticcacaulis.
OX NCBI_TaxID=1282362 {ECO:0000313|EMBL:ESQ85940.1, ECO:0000313|Proteomes:UP000017826};
RN [1] {ECO:0000313|EMBL:ESQ85940.1, ECO:0000313|Proteomes:UP000017826}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AC466 {ECO:0000313|EMBL:ESQ85940.1,
RC ECO:0000313|Proteomes:UP000017826};
RX PubMed=24463524; DOI=10.1038/nature12900;
RA Jiang C., Brown P.J., Ducret A., Brun Y.V.;
RT "Sequential evolution of bacterial morphology by co-option of a
RT developmental regulator.";
RL Nature 506:489-493(2014).
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:ESQ85940.1}.
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DR EMBL; AWGE01000001; ESQ85940.1; -; Genomic_DNA.
DR RefSeq; WP_023456403.1; NZ_AWGE01000001.1.
DR AlphaFoldDB; V4PKH1; -.
DR STRING; 1282362.AEAC466_01800; -.
DR PATRIC; fig|1282362.3.peg.360; -.
DR eggNOG; COG0019; Bacteria.
DR OrthoDB; 9802241at2; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000017826; 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; 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:UP000017826}.
FT DOMAIN 30..381
FT /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF00278"
FT DOMAIN 63..290
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT ACT_SITE 354
FT /note="Proton donor"
FT /evidence="ECO:0000256|PIRSR:PIRSR600183-50"
FT BINDING 248
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 283..286
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 286
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 324
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 328
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 355
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 383
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 383
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT MOD_RES 69
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120,
FT ECO:0000256|PIRSR:PIRSR600183-50"
SQ SEQUENCE 438 AA; 46897 MW; 678D34ACDF0A42C1 CRC64;
MNHFDYQDGA LHCEQVSLTE LAERVGTPLY VYSSATLERH YRVFADALAS KPELHSPKGE
APLVAFACKA NSNLSVLATL AAQGAGADTV SEGEIRKALK AGVPPEKIVF SGVGKTDAEM
AFALQAGIYQ LNVESRPELE RLARVAAELN RVAPFVIRIN PGVGAGGHEK ITTGGAKDKF
GISAAEALKL YADAAGHPNL APMGIACHIG SQILDLTPLQ EAFSRMRGWV EDLRAGGLSV
ERLDLGGGLG VPYFNQKEPA TVADYAEMAA LSVGNLGVRY TFEPGRLIAA NAGVLISKVV
HVHERADSGQ KFLVLDAAMN DLIRPALYDA FHDIRPVARP GNETASYDVV GPVCETGDTF
TRGREMPVMQ TGDLVAFMSA GAYGAVMGSE YNSRPLAPEV LVRDGDWYIV RPRPSYDEMM
AREPMPAWFA AEPKAKIA
//
