DCDA_HELPJ
ID DCDA_HELPJ Reviewed; 405 AA.
AC Q9ZME5;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 1.
DT 03-AUG-2022, entry version 124.
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=jhp_0275;
OS Helicobacter pylori (strain J99 / ATCC 700824) (Campylobacter pylori J99).
OC Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales;
OC Helicobacteraceae; Helicobacter.
OX NCBI_TaxID=85963;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=J99 / ATCC 700824;
RX PubMed=9923682; DOI=10.1038/16495;
RA Alm R.A., Ling L.-S.L., Moir D.T., King B.L., Brown E.D., Doig P.C.,
RA Smith D.R., Noonan B., Guild B.C., deJonge B.L., Carmel G., Tummino P.J.,
RA Caruso A., Uria-Nickelsen M., Mills D.M., Ives C., Gibson R., Merberg D.,
RA Mills S.D., Jiang Q., Taylor D.E., Vovis G.F., Trust T.J.;
RT "Genomic sequence comparison of two unrelated isolates of the human gastric
RT pathogen Helicobacter pylori.";
RL Nature 397:176-180(1999).
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; AE001439; AAD05866.1; -; Genomic_DNA.
DR PIR; F71950; F71950.
DR RefSeq; WP_000483657.1; NZ_CP011330.1.
DR AlphaFoldDB; Q9ZME5; -.
DR SMR; Q9ZME5; -.
DR STRING; 85963.jhp_0275; -.
DR EnsemblBacteria; AAD05866; AAD05866; jhp_0275.
DR KEGG; hpj:jhp_0275; -.
DR PATRIC; fig|85963.30.peg.739; -.
DR eggNOG; COG0019; Bacteria.
DR OMA; YCRSMAS; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000000804; 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; 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.
FT CHAIN 1..405
FT /note="Diaminopimelate decarboxylase"
FT /id="PRO_0000149926"
FT ACT_SITE 329
FT /note="Proton donor"
FT /evidence="ECO:0000255"
FT BINDING 225
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 259..262
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 262
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 298
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 302
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 330
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 358
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 358
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT MOD_RES 46
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
SQ SEQUENCE 405 AA; 45114 MW; 937BE3DBFFADF038 CRC64;
MFNYEELFQT YKTPFYLYDF DKIKQAFLNY KEAFKGRKSL ICYALKANSN LSILSLLANL
GSGADCVSIG EIQRALKAGI KPYKIVFSGV GKSAFEIEQA LKLNILFLNV ESFMELKTIE
TIAQSLGIKA RISIRINPNI DAKTHPYIST GLKENKFGVE EKEALEMFLW AKKSAFLEPV
SVHFHIGSQL LDLDPITEAS QKVAKIAKSL IALGIDLRFF DVGGGIGVSY ENEETIKLYD
YAQGILNSLQ GLDLTIICEP GRSIVAESGE LITQVLYEKK AQNKRFVIVD AGMNDFLRPS
LYHAKHAIRV ITPCGGREIS PCDVVGPVCE SSDTFLKDAN LPELEPGDKL AIEKVGAYGS
SMASQYNSRP KLLELALEDH KIRVIRKREA LEDLWRLEIE GLEGV
