ID I3WG03_BIFBI Unreviewed; 542 AA.
AC I3WG03;
DT 05-SEP-2012, integrated into UniProtKB/TrEMBL.
DT 05-SEP-2012, sequence version 1.
DT 24-JAN-2024, entry version 58.
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 ECO:0000313|EMBL:AFL03816.1};
GN ORFNames=BBB_0220 {ECO:0000313|EMBL:AFL03816.1};
OS Bifidobacterium bifidum BGN4.
OC Bacteria; Actinomycetota; Actinomycetes; Bifidobacteriales;
OC Bifidobacteriaceae; Bifidobacterium.
OX NCBI_TaxID=484020 {ECO:0000313|EMBL:AFL03816.1, ECO:0000313|Proteomes:UP000006173};
RN [1] {ECO:0000313|EMBL:AFL03816.1, ECO:0000313|Proteomes:UP000006173}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=BGN4 {ECO:0000313|EMBL:AFL03816.1,
RC ECO:0000313|Proteomes:UP000006173};
RX PubMed=22887663; DOI=10.1128/JB.00988-12;
RA Yu D.S., Jeong H., Lee D.H., Kwon S.K., Song J.Y., Kim B.K., Park M.S.,
RA Ji G.E., Oh T.K., Kim J.F.;
RT "Complete Genome Sequence of the Probiotic Bacterium Bifidobacterium
RT bifidum Strain BGN4.";
RL J. Bacteriol. 194:4757-4758(2012).
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}.
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DR EMBL; CP001361; AFL03816.1; -; Genomic_DNA.
DR RefSeq; WP_014759797.1; NC_017999.1.
DR AlphaFoldDB; I3WG03; -.
DR KEGG; bbf:BBB_0220; -.
DR PATRIC; fig|484020.3.peg.216; -.
DR HOGENOM; CLU_026444_0_1_11; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000006173; Chromosome.
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; 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, ECO:0000313|EMBL:AFL03816.1};
KW Lysine biosynthesis {ECO:0000256|HAMAP-Rule:MF_02120};
KW Pyridoxal phosphate {ECO:0000256|HAMAP-Rule:MF_02120};
KW Reference proteome {ECO:0000313|Proteomes:UP000006173}.
FT DOMAIN 65..199
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT DOMAIN 291..394
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT DOMAIN 395..498
FT /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF00278"
FT BINDING 345
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 387..390
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 390
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 439
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 443
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 471
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 500
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 500
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT MOD_RES 83
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
SQ SEQUENCE 542 AA; 57785 MW; 902787E14BB30F77 CRC64;
MTGSAVRVDG TQGITPIWPV ATAVNAEGAL TFHGRTAESL LDEFGSPLYL IDTDEVSARA
RYFVRAAADA FTNSTTHVSF AGKAFLSKEV VRLVTDAGML VDTCSMGEMR IALAAGVPGR
RLVLHGNNKS DAEIELAIEQ GFAKIVVDEP GEPARIAAIA RRLGKRARVM LRVTAGIHAG
GHEYISTAHE DQKFGVPLLP AGADAAALSV LDELTADPAG VTPAVTNAHI AERDGDAGDG
NAKPERELHY DVKYPYDLSH EEIPEKDKAL AAAMETVADG PALAVLKDIL TRSDELELVG
IHSHIGSNIH DADAFIQAAK RMMLLRKTFY ATDAYTLPEV DLGGGYSVAY TDGEDSMDVR
VELRRLAEAV GAINRALGVP APAISFEPGR WIVAPAGVTL YRVGTIKPVH LSDAKDKTGN
PIDERVYVSV DGGMSDNIRP ALYGADYTVR LANRRGSDES MLVRVVGMHC ESGDIIVHED
RLPADLRRGD ILAVPVTGAY GRTMASNYNQ ALIPAVVAAS EAGAHVMIRR QTIGDLLDLD
QG
//
