ID C5EDD7_BIFLI Unreviewed; 518 AA.
AC C5EDD7;
DT 28-JUL-2009, integrated into UniProtKB/TrEMBL.
DT 28-JUL-2009, sequence version 1.
DT 24-JAN-2024, entry version 70.
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:EEQ56031.1};
GN ORFNames=BLIG_02160 {ECO:0000313|EMBL:EEQ56031.1};
OS Bifidobacterium longum subsp. infantis CCUG 52486.
OC Bacteria; Actinomycetota; Actinomycetes; Bifidobacteriales;
OC Bifidobacteriaceae; Bifidobacterium.
OX NCBI_TaxID=537937 {ECO:0000313|EMBL:EEQ56031.1};
RN [1] {ECO:0000313|EMBL:EEQ56031.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CCUG 52486 {ECO:0000313|EMBL:EEQ56031.1};
RG The Broad Institute Genome Sequencing Platform;
RA Gougoulias C., Tuohy K.M., Gibson G.R., Ward D., Mehta T., Young S.,
RA Jaffe D., Gnerre S., Berlin A., Heiman D., Hepburn T., Shea T., Sykes S.,
RA Alvarado L., Kodira C., Borodovsky M., Lander E., Galagan J., Nusbaum C.,
RA Birren B.;
RT "Annotation of Bifidobacterium longum subsp. infantis CCUG 52486.";
RL Submitted (AUG-2008) 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}.
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DR EMBL; DS990244; EEQ56031.1; -; Genomic_DNA.
DR AlphaFoldDB; C5EDD7; -.
DR HOGENOM; CLU_026444_0_1_11; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000005084; 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; 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; 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 Lyase {ECO:0000256|HAMAP-Rule:MF_02120, ECO:0000313|EMBL:EEQ56031.1};
KW Lysine biosynthesis {ECO:0000256|HAMAP-Rule:MF_02120};
KW Pyridoxal phosphate {ECO:0000256|HAMAP-Rule:MF_02120}.
FT DOMAIN 41..176
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT DOMAIN 265..369
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT DOMAIN 370..473
FT /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF00278"
FT REGION 200..221
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 320
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 362..365
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 365
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 414
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 418
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 446
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 475
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 475
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT MOD_RES 60
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
SQ SEQUENCE 518 AA; 55503 MW; 82A72222A76D88E7 CRC64;
MNAEGSIEFH GRTAESLLDE FGSPLYLIDT DEVVARARHF VRAAAEAFNT STTHVSFAGK
AFLSKEVVRL VTEAGMFVDT CTMGEMKIAL AAGVPGRRLV LHGNNKSDEE IALAIEQGFA
KIVIDEPDEP ERVAAIARKL GKRARVMLRV TVGVHAGGHE YISTAHEDQK FGVPLLAAGA
DAAVLDVLND LKDVTPAATN ARISATHSPE NGAEKTEKSE RELHYDVKYP YDLSHEEVSD
TDKALAAAME AIADGPSIAV LKTILANQDV LELVGAHSHI GSNIHDADAF IHAAKRMMLL
RKTLWATDAY ILPEIDLGGG YSVAYTDGED SMDIDVELTR LADAVNSTNR ALGMPAPAIS
FEPGRYIVAP AGVTLYRVGT IKHVHLSDAK DSDGNPIAER VYVSVDGGMS DNIRPALYGA
DYTARLANRT GSAETMLARV CGMHCESGDI VVHEVQLPAD LKRGDILAVP VTGAYGRTMA
SNYNQALIPA VVAVSESGAH VMLRRQTVDD LLNLDVSE
//
