ID A0A261F386_9BIFI Unreviewed; 517 AA.
AC A0A261F386;
DT 20-DEC-2017, integrated into UniProtKB/TrEMBL.
DT 20-DEC-2017, sequence version 1.
DT 24-JAN-2024, entry version 22.
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=PSSU_0317 {ECO:0000313|EMBL:OZG53551.1};
OS Pseudoscardovia suis.
OC Bacteria; Actinomycetota; Actinomycetes; Bifidobacteriales;
OC Bifidobacteriaceae; Pseudoscardovia.
OX NCBI_TaxID=987063 {ECO:0000313|EMBL:OZG53551.1, ECO:0000313|Proteomes:UP000216454};
RN [1] {ECO:0000313|EMBL:OZG53551.1, ECO:0000313|Proteomes:UP000216454}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 24744 {ECO:0000313|EMBL:OZG53551.1,
RC ECO:0000313|Proteomes:UP000216454};
RX PubMed=28764658; DOI=10.1186/s12864-017-3955-4;
RA Lugli G.A., Milani C., Turroni F., Duranti S., Mancabelli L.,
RA Mangifesta M., Ferrario C., Modesto M., Mattarelli P., Jiri K.,
RA van Sinderen D., Ventura M.;
RT "Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae
RT family.";
RL BMC Genomics 18:568-568(2017).
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, ECO:0000256|PIRSR:PIRSR600183-50};
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:OZG53551.1}.
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DR EMBL; MWWQ01000004; OZG53551.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A261F386; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000216454; 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; 2.
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 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 PRINTS; PR01179; ODADCRBXLASE.
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|ARBA:ARBA00023154, ECO:0000256|HAMAP-
KW Rule:MF_02120};
KW Pyridoxal phosphate {ECO:0000256|HAMAP-Rule:MF_02120,
KW ECO:0000256|PIRSR:PIRSR600183-50};
KW Reference proteome {ECO:0000313|Proteomes:UP000216454}.
FT DOMAIN 69..202
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT DOMAIN 203..472
FT /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF00278"
FT DOMAIN 267..376
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT REGION 222..244
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 444
FT /note="Proton donor"
FT /evidence="ECO:0000256|PIRSR:PIRSR600183-50"
FT BINDING 328
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 369..372
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 372
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 413
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 417
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 445
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 474
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 474
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT MOD_RES 87
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120,
FT ECO:0000256|PIRSR:PIRSR600183-50"
SQ SEQUENCE 517 AA; 55540 MW; FE25278B1A774C13 CRC64;
MNATNPPSGA GVAGATKMSA VWPAATRRDA QGNISFHGYD ALDLVQRYGS PLYVMDTDEV
RRRAKYFVEA ARNAFPNTTT HVSFAAKAFI SKEICRIVAE EGMTIDTCTL GEMRIALAAG
VPGRRLVLHG NNKTDEEIAL AIDNDFAKIV LDSPDEAARV ERIARAHDKR AKVMLRVTVG
VHAGGHEYIS TAHEDQKFGV PLLAPGASAS VLTGEYDRPD EVEHASEAEP DDAPRINSLY
AIPPSKKDRN PKLEAALNAL ADGPAIAALK DIRKRDDYLE LVGVHSHIGS QIHDADAFIE
AVGRVLLLRK TFYATDGYVL PEIDLGGGYS VPYLDSDSSM DVAATLRRIA KAFTAEIMKG
LPAPVVSFEP GRFIVGPAGV TLYRVGTVKP VVLSDGTTRT YVSVDGGMSD NIRPALYGAD
YEVELANRVG SGTKMLARVV GKHCESGDIV VKDCHLPADI KRGDILAVPV TGAYGRTMAS
NYNQALRPAV VAVSHDGSHV MIRRETIDDL LGLDVSQ
//
