DCDA_STAAC
ID DCDA_STAAC Reviewed; 421 AA.
AC Q5HG20;
DT 27-JUL-2011, integrated into UniProtKB/Swiss-Prot.
DT 15-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 114.
DE RecName: Full=Diaminopimelate decarboxylase;
DE Short=DAP decarboxylase;
DE Short=DAPDC;
DE EC=4.1.1.20;
GN Name=lysA; OrderedLocusNames=SACOL1435;
OS Staphylococcus aureus (strain COL).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=93062;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=COL;
RX PubMed=15774886; DOI=10.1128/jb.187.7.2426-2438.2005;
RA Gill S.R., Fouts D.E., Archer G.L., Mongodin E.F., DeBoy R.T., Ravel J.,
RA Paulsen I.T., Kolonay J.F., Brinkac L.M., Beanan M.J., Dodson R.J.,
RA Daugherty S.C., Madupu R., Angiuoli S.V., Durkin A.S., Haft D.H.,
RA Vamathevan J.J., Khouri H., Utterback T.R., Lee C., Dimitrov G., Jiang L.,
RA Qin H., Weidman J., Tran K., Kang K.H., Hance I.R., Nelson K.E.,
RA Fraser C.M.;
RT "Insights on evolution of virulence and resistance from the complete genome
RT analysis of an early methicillin-resistant Staphylococcus aureus strain and
RT a biofilm-producing methicillin-resistant Staphylococcus epidermidis
RT strain.";
RL J. Bacteriol. 187:2426-2438(2005).
RN [2]
RP DISRUPTION PHENOTYPE.
RC STRAIN=COL;
RX PubMed=10566865; DOI=10.1089/mdr.1999.5.163;
RA de Lencastre H., Wu S.-W., Pinho M.G., Ludovice A.M., Filipe S.,
RA Gardete S., Sobral R., Gill S.R., Chung M., Tomasz A.;
RT "Antibiotic resistance as a stress response: complete sequencing of a large
RT number of chromosomal loci in Staphylococcus aureus strain COL that impact
RT on the expression of resistance to methicillin.";
RL Microb. Drug Resist. 5:163-175(1999).
CC -!- FUNCTION: Specifically catalyzes the decarboxylation of meso-
CC diaminopimelate (meso-DAP) to L-lysine (By similarity). Plays a role in
CC beta-lactam antibiotic resistance. {ECO:0000250}.
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 -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000250};
CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC pathway; L-lysine from DL-2,6-diaminopimelate: step 1/1.
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- DISRUPTION PHENOTYPE: Disruption of this gene does not affect growth in
CC rich organic media but reduces the level of methicillin resistance by
CC nearly 100-fold. {ECO:0000269|PubMed:10566865}.
CC -!- SIMILARITY: Belongs to the Orn/Lys/Arg decarboxylase class-II family.
CC LysA subfamily. {ECO:0000305}.
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DR EMBL; CP000046; AAW38180.1; -; Genomic_DNA.
DR RefSeq; WP_000216946.1; NC_002951.2.
DR AlphaFoldDB; Q5HG20; -.
DR SMR; Q5HG20; -.
DR PRIDE; Q5HG20; -.
DR EnsemblBacteria; AAW38180; AAW38180; SACOL1435.
DR KEGG; sac:SACOL1435; -.
DR HOGENOM; CLU_026444_0_1_9; -.
DR OMA; YCRSMAS; -.
DR SABIO-RK; Q5HG20; -.
DR UniPathway; UPA00034; UER00027.
DR Proteomes; UP000000530; 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 GO; GO:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
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; Antibiotic resistance; Decarboxylase; Lyase;
KW Lysine biosynthesis; Pyridoxal phosphate.
FT CHAIN 1..421
FT /note="Diaminopimelate decarboxylase"
FT /id="PRO_0000411131"
FT ACT_SITE 349
FT /note="Proton donor"
FT /evidence="ECO:0000255"
FT BINDING 237
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT BINDING 279..282
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT BINDING 282
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 319
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 323
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 350
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 379
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT BINDING 379
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT MOD_RES 62
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250"
SQ SEQUENCE 421 AA; 47035 MW; 8F06E7C8A9078075 CRC64;
MTVKYNQNGE LTMDGISLKT IAQSFGTPTI VYDELQIREQ MRRYHRAFKD SGLKYNISYA
SKAFTCIQMV KLVAEEDLQL DVVSEGELYT ALEAGFEPSR IHFHGNNKTK HEIRYALENN
IGYFVIDSLE EIELIDRYAN DTVQVVLRVN PGVEAHTHEF IQTGQEDSKF GLSIQYGLAK
KAIDKVQQSK HLKLKGVHCH IGSQIEGTEA FIETAKIVLR WLKEQGIQVE LLNLGGGFGI
KYVEGDESFP IESGIKDITD AIKSEIKVLG IDAPEIGIEP GRSIVGEAGV TLYEVGTIKE
IPEINKYVSI DGGMSDHIRT ALYDAKYQAL LVNRNEEADD SVTIAGKLCE SGDIIIKDAK
LPSSVKRGDY LAILSTGAYH YSMASNYNQM QKPSVFFLKD GKAREVIKRQ SLRQLIINDT
K
