ID B3R7C8_CUPTR Unreviewed; 419 AA.
AC B3R7C8;
DT 02-SEP-2008, integrated into UniProtKB/TrEMBL.
DT 02-SEP-2008, sequence version 1.
DT 27-MAR-2024, entry version 105.
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 ECO:0000313|EMBL:CAQ70828.1};
GN OrderedLocusNames=RALTA_A2903 {ECO:0000313|EMBL:CAQ70828.1};
OS Cupriavidus taiwanensis (strain DSM 17343 / BCRC 17206 / CCUG 44338 / CIP
OS 107171 / LMG 19424 / R1) (Ralstonia taiwanensis (strain LMG 19424)).
OC Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Cupriavidus.
OX NCBI_TaxID=977880 {ECO:0000313|EMBL:CAQ70828.1, ECO:0000313|Proteomes:UP000001692};
RN [1] {ECO:0000313|EMBL:CAQ70828.1, ECO:0000313|Proteomes:UP000001692}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 17343 / BCRC 17206 / CCUG 44338 / CIP 107171 / LMG 19424 /
RC R1 {ECO:0000313|Proteomes:UP000001692};
RX PubMed=18490699; DOI=10.1101/gr.076448.108;
RA Amadou C., Pascal G., Mangenot S., Glew M., Bontemps C., Capela D.,
RA Carrere S., Cruveiller S., Dossat C., Lajus A., Marchetti M., Poinsot V.,
RA Rouy Z., Servin B., Saad M., Schenowitz C., Barbe V., Batut J., Medigue C.,
RA Masson-Boivin C.;
RT "Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and
RT comparative genomics of rhizobia.";
RL Genome Res. 18:1472-1483(2008).
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}.
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DR EMBL; CU633749; CAQ70828.1; -; Genomic_DNA.
DR RefSeq; WP_012354119.1; NC_010528.1.
DR AlphaFoldDB; B3R7C8; -.
DR GeneID; 29760575; -.
DR KEGG; cti:RALTA_A2903; -.
DR eggNOG; COG0019; Bacteria.
DR HOGENOM; CLU_026444_0_0_4; -.
DR BioCyc; CTAI977880:RALTA_RS14150-MONOMER; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000001692; Chromosome 1.
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 31..372
FT /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF00278"
FT DOMAIN 39..283
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT ACT_SITE 346
FT /note="Proton donor"
FT /evidence="ECO:0000256|PIRSR:PIRSR600183-50"
FT BINDING 240
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 277..280
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 280
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 316
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 320
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 347
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 374
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT BINDING 374
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120"
FT MOD_RES 61
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_02120,
FT ECO:0000256|PIRSR:PIRSR600183-50"
SQ SEQUENCE 419 AA; 45112 MW; 9CC1CE78BC9AD81B CRC64;
MTAFFHRQDG ALAVEQVPLA RIAAEFGTPT YVYSRAALTA AYQAYAAACA GRKAQVQYAM
KANSNLAVLQ VFARLGAGFD IVSGGELKRV LAAGGDPRKV VFSGVGKSAA EMELALAQDV
RCFNVESIPE LDRLNEVAGR VGKRARVSLR INPDVDARTH PYISTGLKGN KFGIAFEDVL
PTYRAAAALP HLAVTGIDCH IGSQITEVEP YLEALDKVLD VVEALEREGI SLEHIDVGGG
LGITYTDETP PDITGFATTL LERVAARGHG HREVLFEPGR SLVGNAGVLL TQVEFLKPGA
AKNFCIVDAA MNDLARPAMY EAYHRIEPVA LRDGAAVTYD IVGPVCESGD WLGRDRALAV
QPGDLLAVMS AGAYGFTMSS NYNTRPRAAE VMVDGARVHL VRERELVEDL FRDERLLQD
//
