DCDA_MYCS2
ID DCDA_MYCS2 Reviewed; 474 AA.
AC Q9X5M1; A0R222; I7GD81;
DT 21-FEB-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 130.
DE RecName: Full=Diaminopimelate decarboxylase {ECO:0000255|HAMAP-Rule:MF_02120};
DE Short=DAP decarboxylase {ECO:0000255|HAMAP-Rule:MF_02120};
DE Short=DAPDC {ECO:0000255|HAMAP-Rule:MF_02120};
DE EC=4.1.1.20 {ECO:0000255|HAMAP-Rule:MF_02120};
GN Name=lysA {ECO:0000255|HAMAP-Rule:MF_02120};
GN OrderedLocusNames=MSMEG_4958, MSMEI_4831;
OS Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium
OS smegmatis).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycolicibacterium.
OX NCBI_TaxID=246196;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Pavelka M.S. Jr., Jacobs W.R. Jr.;
RT "A comparison of the construction of unmarked deletion mutations in
RT Mycobacterium smegmatis, M. bovis bacille Calmette-Guerin (BCG) and M.
RT tuberculosis H37Rv by allelic exchange.";
RL Submitted (FEB-1999) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700084 / mc(2)155;
RA Fleischmann R.D., Dodson R.J., Haft D.H., Merkel J.S., Nelson W.C.,
RA Fraser C.M.;
RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700084 / mc(2)155;
RX PubMed=17295914; DOI=10.1186/gb-2007-8-2-r20;
RA Deshayes C., Perrodou E., Gallien S., Euphrasie D., Schaeffer C.,
RA Van-Dorsselaer A., Poch O., Lecompte O., Reyrat J.-M.;
RT "Interrupted coding sequences in Mycobacterium smegmatis: authentic
RT mutations or sequencing errors?";
RL Genome Biol. 8:R20.1-R20.9(2007).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700084 / mc(2)155;
RX PubMed=18955433; DOI=10.1101/gr.081901.108;
RA Gallien S., Perrodou E., Carapito C., Deshayes C., Reyrat J.-M.,
RA Van Dorsselaer A., Poch O., Schaeffer C., Lecompte O.;
RT "Ortho-proteogenomics: multiple proteomes investigation through orthology
RT and a new MS-based protocol.";
RL Genome Res. 19:128-135(2009).
CC -!- FUNCTION: Specifically catalyzes the decarboxylation of meso-
CC diaminopimelate (meso-DAP) to L-lysine. {ECO:0000255|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:0000255|HAMAP-Rule:MF_02120};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000255|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:0000255|HAMAP-Rule:MF_02120}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_02120}.
CC -!- SIMILARITY: Belongs to the Orn/Lys/Arg decarboxylase class-II family.
CC LysA subfamily. {ECO:0000255|HAMAP-Rule:MF_02120}.
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DR EMBL; AF126720; AAD32591.1; -; Genomic_DNA.
DR EMBL; CP000480; ABK70119.1; -; Genomic_DNA.
DR EMBL; CP001663; AFP41276.1; -; Genomic_DNA.
DR RefSeq; WP_011730213.1; NZ_SIJM01000019.1.
DR RefSeq; YP_889210.1; NC_008596.1.
DR AlphaFoldDB; Q9X5M1; -.
DR SMR; Q9X5M1; -.
DR STRING; 246196.MSMEI_4831; -.
DR EnsemblBacteria; ABK70119; ABK70119; MSMEG_4958.
DR EnsemblBacteria; AFP41276; AFP41276; MSMEI_4831.
DR GeneID; 66736279; -.
DR KEGG; msg:MSMEI_4831; -.
DR KEGG; msm:MSMEG_4958; -.
DR PATRIC; fig|246196.19.peg.4837; -.
DR eggNOG; COG0019; Bacteria.
DR OMA; YCRSMAS; -.
DR OrthoDB; 861683at2; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000000757; Chromosome.
DR Proteomes; UP000006158; 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; 2.40.37.10; -; 1.
DR Gene3D; 3.20.20.10; -; 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; IPR022653; De-COase2_pyr-phos_BS.
DR InterPro; IPR000183; Orn/DAP/Arg_de-COase.
DR InterPro; IPR029066; PLP-binding_barrel.
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; SSF50621; 1.
DR SUPFAM; SSF51419; SSF51419; 1.
DR TIGRFAMs; TIGR01048; lysA; 1.
DR PROSITE; PS00878; ODR_DC_2_1; 1.
DR PROSITE; PS00879; ODR_DC_2_2; 1.
PE 3: Inferred from homology;
KW Amino-acid biosynthesis; Decarboxylase; Lyase; Lysine biosynthesis;
KW Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..474
FT /note="Diaminopimelate decarboxylase"
FT /id="PRO_0000149927"
FT REGION 1..25
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 8..23
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 400
FT /note="Proton donor"
FT /evidence="ECO:0000255"
FT BINDING 283
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 325..328
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 328
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 369
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 373
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 401
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 430
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 430
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT MOD_RES 97
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
SQ SEQUENCE 474 AA; 50348 MW; 442D9ECDF771C7BB CRC64;
MNAHPAGPRH AEELHHADVP DKPQSPDEIM LLAPNVWPRN LVRGADGVVT IAGVPVTDLA
AKFGTPLFVI DEDDFRTRCR DIAAAFGGGQ YVHYAAKAFL CSEIARWVDE EGLSLDVATG
GELAVALHAG FPASRITVHG NNKSVAELTA AVQAGVGHVV LDSEIEIERL DQIAGAAGVV
QDVLVRVTVG VEAHTHEFIS TAHEDQKFGL SLATGAAMNA IRRVFATDNL RLVGLHSHIG
SQIFDVAGFE IAAHRVIGLL RDVVAEFGVE KTSQMSIVDL GGGLGISYLP HDDPPPMKEL
ADKLLEIVRT ESAAVGLPTP KLVVEPGRAI AGPGTITLYE VGTVKDVAVS QTAHRRYVSV
DGGMSDNIRT SLYAAQYDAR LVSRVSDAPP ALARIVGKHC ESGDIVVRDT WVSDDIAPGD
LIGVAATGAY CYSMSSRYNL LCRPAVVAVA DGQARLVLRR ETVEDLLSLE VKGQ
