ID A0A1A9RTF3_9NEIS Unreviewed; 406 AA.
AC A0A1A9RTF3;
DT 05-OCT-2016, integrated into UniProtKB/TrEMBL.
DT 05-OCT-2016, sequence version 1.
DT 24-JAN-2024, entry version 28.
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=A7P95_10025 {ECO:0000313|EMBL:OAM26044.1};
OS Eikenella longinqua.
OC Bacteria; Pseudomonadota; Betaproteobacteria; Neisseriales; Neisseriaceae;
OC Eikenella.
OX NCBI_TaxID=1795827 {ECO:0000313|EMBL:OAM26044.1, ECO:0000313|Proteomes:UP000077885};
RN [1] {ECO:0000313|Proteomes:UP000077885}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NML02-A-017 {ECO:0000313|Proteomes:UP000077885};
RA Bernier A.-M., Bernard K.;
RT "Draft genome of Corynebacterium afermentans subsp. afermentans LCDC
RT 88199T.";
RL Submitted (MAY-2016) 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:OAM26044.1}.
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DR EMBL; LXSL01000032; OAM26044.1; -; Genomic_DNA.
DR RefSeq; WP_067594842.1; NZ_LXSL01000032.1.
DR AlphaFoldDB; A0A1A9RTF3; -.
DR STRING; 1795827.A7P95_10025; -.
DR OrthoDB; 9802241at2; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000077885; 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; 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; 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}.
FT DOMAIN 29..271
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT DOMAIN 272..360
FT /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF00278"
FT ACT_SITE 334
FT /note="Proton donor"
FT /evidence="ECO:0000256|PIRSR:PIRSR600183-50"
FT BINDING 231
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 265..268
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 268
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 304
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 308
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 335
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 362
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 362
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT MOD_RES 52
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120,
FT ECO:0000256|PIRSR:PIRSR600183-50"
SQ SEQUENCE 406 AA; 43344 MW; 6A0154EF74828550 CRC64;
MSLYCENVSL DALAEQFGTP LYVYSQAALT EAYQSYTAAF SGLNPLLCYA VKANGNLSIL
RHFARLGSGF DIVSGGELAR VLAAGGRADK TIFSGVGKSR AEMVYALEAG IKCFNVESLP
ELDQLNEAAA GLGTVAPVSL RINPDVDAQT HPYISTGLKA NKFGIAMEDA EAAYRHAASL
PHLRITGIDC HIGSQLTNLA PLVEACERML ALVDRLAAQG IELEHIDLGG GISIVYHDET
PPDLPAYAQA LRQLLGGRKL SLILEPGRSL VGNAGLLLTR VERVKRNGDK HFVIADAAMN
DLMRPALYQA YHHIDNTNPQ PGAPFTADIV GPVCETGDFL AQNRRIAAQA GDLLVVHSAG
AYAASMASNY NTRARAAEVL VNGSEFRLVR AREQITDMLA GELACL
//
