DCDA_NEIMB
ID DCDA_NEIMB Reviewed; 414 AA.
AC Q9JXM2;
DT 21-FEB-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 119.
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}; OrderedLocusNames=NMB1976;
OS Neisseria meningitidis serogroup B (strain MC58).
OC Bacteria; Proteobacteria; Betaproteobacteria; Neisseriales; Neisseriaceae;
OC Neisseria.
OX NCBI_TaxID=122586;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MC58;
RX PubMed=10710307; DOI=10.1126/science.287.5459.1809;
RA Tettelin H., Saunders N.J., Heidelberg J.F., Jeffries A.C., Nelson K.E.,
RA Eisen J.A., Ketchum K.A., Hood D.W., Peden J.F., Dodson R.J., Nelson W.C.,
RA Gwinn M.L., DeBoy R.T., Peterson J.D., Hickey E.K., Haft D.H.,
RA Salzberg S.L., White O., Fleischmann R.D., Dougherty B.A., Mason T.M.,
RA Ciecko A., Parksey D.S., Blair E., Cittone H., Clark E.B., Cotton M.D.,
RA Utterback T.R., Khouri H.M., Qin H., Vamathevan J.J., Gill J., Scarlato V.,
RA Masignani V., Pizza M., Grandi G., Sun L., Smith H.O., Fraser C.M.,
RA Moxon E.R., Rappuoli R., Venter J.C.;
RT "Complete genome sequence of Neisseria meningitidis serogroup B strain
RT MC58.";
RL Science 287:1809-1815(2000).
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; AE002098; AAF42304.1; -; Genomic_DNA.
DR PIR; A81020; A81020.
DR RefSeq; NP_274969.1; NC_003112.2.
DR RefSeq; WP_002225849.1; NC_003112.2.
DR AlphaFoldDB; Q9JXM2; -.
DR SMR; Q9JXM2; -.
DR STRING; 122586.NMB1976; -.
DR PaxDb; Q9JXM2; -.
DR EnsemblBacteria; AAF42304; AAF42304; NMB1976.
DR KEGG; nme:NMB1976; -.
DR PATRIC; fig|122586.8.peg.2518; -.
DR HOGENOM; CLU_026444_0_0_4; -.
DR OMA; YCRSMAS; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000000425; Chromosome.
DR GO; GO:0008836; F:diaminopimelate decarboxylase activity; IBA:GO_Central.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IBA:GO_Central.
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; 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; 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..414
FT /note="Diaminopimelate decarboxylase"
FT /id="PRO_0000149932"
FT ACT_SITE 334
FT /note="Proton donor"
FT /evidence="ECO:0000255"
FT BINDING 231
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 265..268
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 268
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 304
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 308
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 335
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 362
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 362
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT MOD_RES 52
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
SQ SEQUENCE 414 AA; 44698 MW; A8AE27C1B81D6CB2 CRC64;
MTLFCEQVPY PRLAEAFGTP LYVYSQSALT EAFEHYQTAF AALNPLVCYA VKANGNLSII
KHFASLGSGF DIVSGGELAR VLAAGGDAAK TIFSGVGKSE AEIEFALNAG VKCFNMESIP
EIDRIQKVAA RLGKTAPVSL RINPDVDAKT HPYISTGLKA NKFGIAYADA LEAYHYAAQQ
PNLKIIGIDC HIGSQLTDLS PLVEACERIL ILVDALAAEG IVLEHLDLGG GVGIVYQDEN
VPDLGAYAQA VQKLIGTRRL KLILEPGRSL VGNAGSLLTR VEFVKYGEEK NFVMVDAAMN
DLMRPALYDA YHHIEAVETK DIATLTANIV GPICETGDFL GKDRTIACEE GDLLLIRSAG
AYGASMASNY NARNRAAEVL VDGNEYRLIR RRETLEQQMA NELACLQAEH QNAV
