ID R6VRI0_9BACT Unreviewed; 387 AA.
AC R6VRI0;
DT 24-JUL-2013, integrated into UniProtKB/TrEMBL.
DT 24-JUL-2013, sequence version 1.
DT 24-JAN-2024, entry version 39.
DE RecName: Full=Diaminopimelate decarboxylase {ECO:0000256|RuleBase:RU003738};
DE EC=4.1.1.20 {ECO:0000256|RuleBase:RU003738};
GN ORFNames=BN576_02015 {ECO:0000313|EMBL:CDC96964.1};
OS Alistipes sp. CAG:268.
OC Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Rikenellaceae;
OC Alistipes.
OX NCBI_TaxID=1262693 {ECO:0000313|EMBL:CDC96964.1, ECO:0000313|Proteomes:UP000018329};
RN [1] {ECO:0000313|EMBL:CDC96964.1, ECO:0000313|Proteomes:UP000018329}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MGS:268 {ECO:0000313|Proteomes:UP000018329};
RA Nielsen H.B., Almeida M., Juncker A.S., Rasmussen S., Li J., Sunagawa S.,
RA Plichta D., Gautier L., Le Chatelier E., Peletier E., Bonde I., Nielsen T.,
RA Manichanh C., Arumugam M., Batto J., Santos M.B.Q.D., Blom N., Borruel N.,
RA Burgdorf K.S., Boumezbeur F., Casellas F., Dore J., Guarner F., Hansen T.,
RA Hildebrand F., Kaas R.S., Kennedy S., Kristiansen K., Kultima J.R.,
RA Leonard P., Levenez F., Lund O., Moumen B., Le Paslier D., Pons N.,
RA Pedersen O., Prifti E., Qin J., Raes J., Tap J., Tims S., Ussery D.W.,
RA Yamada T., MetaHit consortium, Renault P., Sicheritz-Ponten T., Bork P.,
RA Wang J., Brunak S., Ehrlich S.D.;
RT "Dependencies among metagenomic species, viruses, plasmids and units of
RT genetic variation.";
RL Submitted (NOV-2012) to the EMBL/GenBank/DDBJ databases.
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|RuleBase:RU003738};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000256|ARBA:ARBA00001933,
CC ECO:0000256|PIRSR:PIRSR600183-50, 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|RuleBase:RU003738}.
CC -!- SIMILARITY: Belongs to the Orn/Lys/Arg decarboxylase class-II family.
CC {ECO:0000256|RuleBase:RU003737}.
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:CDC96964.1}.
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DR EMBL; CBGE010000098; CDC96964.1; -; Genomic_DNA.
DR AlphaFoldDB; R6VRI0; -.
DR STRING; 1262693.BN576_02015; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000018329; Unassembled WGS sequence.
DR GO; GO:0008836; F:diaminopimelate decarboxylase activity; IEA:UniProtKB-EC.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IEA:UniProtKB-UniPathway.
DR CDD; cd06828; PLPDE_III_DapDC; 1.
DR Gene3D; 3.20.20.10; Alanine racemase; 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; 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; PS00878; ODR_DC_2_1; 1.
PE 3: Inferred from homology;
KW Amino-acid biosynthesis {ECO:0000256|RuleBase:RU003738};
KW Decarboxylase {ECO:0000256|RuleBase:RU003738};
KW Lyase {ECO:0000256|RuleBase:RU003738};
KW Lysine biosynthesis {ECO:0000256|RuleBase:RU003738};
KW Pyridoxal phosphate {ECO:0000256|PIRSR:PIRSR600183-50};
KW Reference proteome {ECO:0000313|Proteomes:UP000018329}.
FT DOMAIN 17..362
FT /note="Orn/DAP/Arg decarboxylase 2 C-terminal"
FT /evidence="ECO:0000259|Pfam:PF00278"
FT DOMAIN 41..271
FT /note="Orn/DAP/Arg decarboxylase 2 N-terminal"
FT /evidence="ECO:0000259|Pfam:PF02784"
FT ACT_SITE 335
FT /note="Proton donor"
FT /evidence="ECO:0000256|PIRSR:PIRSR600183-50"
FT MOD_RES 48
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000256|PIRSR:PIRSR600183-50"
SQ SEQUENCE 387 AA; 42989 MW; EC4F88B815A6E554 CRC64;
MLSRQIASRL RGYETPFYLY DTALLRQTLE SVVYESNKYG YKVHYAIKAN YDDHLLAIIR
EYGLGIDCAS GNELRKAVEA GFAPEGIVYA GVGKRDKELR YAIEQGIMAI NCESIGELEV
VDALSAEAGR VTDVALRINP DIDPKTNHCI DTGQADSKFG ISYEEVLEHA AEIKSLAHIN
IVGIHLHIGS QIRELHVFEN MCNKVNVIVE NLERLGFTFR FVDVGGGLGV NYDVPENEPI
PNFASLFSIV HNHLRVDDKE VHFEFGRSIV AECGELITTV LFNKTTATGR KLVIVDASMT
ELIRPALYGS YHNIENITAD EDAPRDKYTV VGTACESTDV FDQNVSLRRT QRGDLLTIKS
AGAYGMSMAS RYNLHDLPGA VYSDEIK
//
