ID A0A229VX98_9BIFI Unreviewed; 539 AA.
AC A0A229VX98;
DT 25-OCT-2017, integrated into UniProtKB/TrEMBL.
DT 25-OCT-2017, sequence version 1.
DT 24-JAN-2024, entry version 23.
DE RecName: Full=Diaminopimelate decarboxylase {ECO:0000256|HAMAP-Rule:MF_02120};
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};
GN Name=lysA {ECO:0000256|HAMAP-Rule:MF_02120};
GN ORFNames=Tam10B_1472 {ECO:0000313|EMBL:OXN00249.1};
OS Bifidobacterium vansinderenii.
OC Bacteria; Actinomycetota; Actinomycetes; Bifidobacteriales;
OC Bifidobacteriaceae; Bifidobacterium.
OX NCBI_TaxID=1984871 {ECO:0000313|EMBL:OXN00249.1, ECO:0000313|Proteomes:UP000215433};
RN [1] {ECO:0000313|EMBL:OXN00249.1, ECO:0000313|Proteomes:UP000215433}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tam10B {ECO:0000313|EMBL:OXN00249.1,
RC ECO:0000313|Proteomes:UP000215433};
RA Lugli G.A., Duranti S., Mangifesta M.;
RT "Bifidobacterium vansinderenii sp. nov.";
RL Submitted (MAY-2017) 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 -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000256|ARBA:ARBA00001933,
CC ECO:0000256|HAMAP-Rule:MF_02120};
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}.
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:OXN00249.1}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; NEWD01000019; OXN00249.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A229VX98; -.
DR OrthoDB; 9802241at2; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000215433; 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; IPR029066; PLP-binding_barrel.
DR PANTHER; PTHR43727; DIAMINOPIMELATE DECARBOXYLASE; 1.
DR PANTHER; PTHR43727:SF2; DIAMINOPIMELATE DECARBOXYLASE 1, CHLOROPLASTIC-RELATED; 1.
DR Pfam; PF02784; Orn_Arg_deC_N; 2.
DR Pfam; PF00278; Orn_DAP_Arg_deC; 1.
DR SUPFAM; SSF50621; Alanine racemase C-terminal domain-like; 1.
DR SUPFAM; SSF51419; PLP-binding barrel; 2.
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 Lyase {ECO:0000256|HAMAP-Rule:MF_02120};
KW Lysine biosynthesis {ECO:0000256|HAMAP-Rule:MF_02120};
KW Pyridoxal phosphate {ECO:0000256|HAMAP-Rule:MF_02120}.
FT DOMAIN 67..200
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT DOMAIN 287..391
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT DOMAIN 392..495
FT /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF00278"
FT BINDING 342
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 384..387
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 387
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 436
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 440
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 468
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 497
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 497
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT MOD_RES 85
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
SQ SEQUENCE 539 AA; 57518 MW; 53A500EB94DA4815 CRC64;
MSEKTAEQDY ELGKGITPIW PTATTINDDG AIEFHGRTAE SLLSEFGSPL YLIDTDEVAA
RARYFVRAAA DAFNNSTTHV SFAGKAFLSK RVVREVIDAG MLVDTCTMGE MRIALAAGAP
GRRLVLHGNN KSNAEIELAV ENGFAKIVID SADEPARIAE IAHRLGKRAK VMLRVTSGIH
AGGHEYISTA HEDQKFGVPL LPAGADTSAL GVLDDLGDVT PAATNARLSN AANAADKTGK
PERELRYDVK YPYDLSHEEV SDADKALAAA MTTVADGPAL AVLKDILAHS EDLELVGIHS
HIGSNIHDAD AFIQAAKRMM LLRKTFYATD AYTLPEVDLG GGYSVAYTDG EDSMDVRVEL
KRLADAVVAV NRALGMPAPS ISFEPGRWIV APAGVTLYRV GTVKPVRLAD AKDSAGNPIH
ERVYVSVDGG MSDNIRPALY GADYTARLAN RTGSAETMLA RVVGMHCESG DIVVHEVRLP
ADTHRGDILA VPVTGAYGRT MASNYNQALI PAVVGVGESG ASVMIRRQTV DDLLELDQD
//
