DCDA_NEIMA
ID DCDA_NEIMA Reviewed; 406 AA.
AC Q9JWA6; A1IPS9;
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=NMA0468;
OS Neisseria meningitidis serogroup A / serotype 4A (strain DSM 15465 /
OS Z2491).
OC Bacteria; Proteobacteria; Betaproteobacteria; Neisseriales; Neisseriaceae;
OC Neisseria.
OX NCBI_TaxID=122587;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 15465 / Z2491;
RX PubMed=10761919; DOI=10.1038/35006655;
RA Parkhill J., Achtman M., James K.D., Bentley S.D., Churcher C.M.,
RA Klee S.R., Morelli G., Basham D., Brown D., Chillingworth T., Davies R.M.,
RA Davis P., Devlin K., Feltwell T., Hamlin N., Holroyd S., Jagels K.,
RA Leather S., Moule S., Mungall K.L., Quail M.A., Rajandream M.A.,
RA Rutherford K.M., Simmonds M., Skelton J., Whitehead S., Spratt B.G.,
RA Barrell B.G.;
RT "Complete DNA sequence of a serogroup A strain of Neisseria meningitidis
RT Z2491.";
RL Nature 404:502-506(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; AL157959; CAM07750.1; -; Genomic_DNA.
DR PIR; D81964; D81964.
DR RefSeq; WP_010981083.1; NC_003116.1.
DR AlphaFoldDB; Q9JWA6; -.
DR SMR; Q9JWA6; -.
DR EnsemblBacteria; CAM07750; CAM07750; NMA0468.
DR KEGG; nma:NMA0468; -.
DR HOGENOM; CLU_026444_0_0_4; -.
DR OMA; YCRSMAS; -.
DR BioCyc; NMEN122587:NMA_RS02375-MON; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000000626; 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; 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.
FT CHAIN 1..406
FT /note="Diaminopimelate decarboxylase"
FT /id="PRO_0000149931"
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 406 AA; 43796 MW; 198BAE7D88D84496 CRC64;
MTLFCEQVPY PRLAEAFGTP LYVYSQSALT EAFEHYQTAF AELSPLVCYA VKANGNLSII
KHFASLGSGF DIVSGGELAR VLAAGGDAAK TIFSGVGKSE AEIEFALNAG VKCFNMESIP
EIDRIQKVAA RLGKTASVSL RVNPDVDAKT HPYISTGLKA NKFGIAYADA LEAYRHAAQQ
PNLKIIGIDC HIGSQLTDLS PLVEACERIL ILVDALAAEG IVLEHLDLGG GVGIVYQDED
VPDLGAYAQA VQKLIGTRRL KLILEPGRSL VGNAGALLTR VEFVKYGEEK NFVMVDAAMN
DLMRPALYDA YHHIEAVEPK NIAPLTANIV GPICETGDFL GKDRTIACEE GDLLLIRSAG
AYGASMASNY NARNRAAEVL VDGNEYRLIR RRETLEQQMA NELACL
