DCDA_HELPX
ID DCDA_HELPX Reviewed; 405 AA.
AC B4XMC6;
DT 27-JUL-2011, integrated into UniProtKB/Swiss-Prot.
DT 23-SEP-2008, sequence version 1.
DT 03-AUG-2022, entry version 57.
DE RecName: Full=Diaminopimelate decarboxylase {ECO:0000255|HAMAP-Rule:MF_02120, ECO:0000303|PubMed:18508763};
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, ECO:0000269|PubMed:18508763};
GN Name=lysA {ECO:0000255|HAMAP-Rule:MF_02120};
OS Helicobacter pylori (Campylobacter pylori).
OC Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales;
OC Helicobacteraceae; Helicobacter.
OX NCBI_TaxID=210;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF
RP WILD-TYPE AND MUTANT LEU-148 IN COMPLEX WITH PLP AND LYSINE, FUNCTION,
RP CATALYTIC ACTIVITY, KINETIC PARAMETERS, COFACTOR, SUBUNIT, CATALYTIC
RP MECHANISM, ACTIVE SITE, AND MUTAGENESIS OF ILE-148.
RC STRAIN=SS1;
RX PubMed=18508763; DOI=10.1074/jbc.m801823200;
RA Hu T., Wu D., Chen J., Ding J., Jiang H., Shen X.;
RT "The catalytic intermediate stabilized by a 'down' active site loop for
RT diaminopimelate decarboxylase from Helicobacter pylori. Enzymatic
RT characterization with crystal structure analysis.";
RL J. Biol. Chem. 283:21284-21293(2008).
CC -!- FUNCTION: Specifically catalyzes the decarboxylation of meso-
CC diaminopimelate (meso-DAP) to L-lysine. {ECO:0000255|HAMAP-
CC Rule:MF_02120, ECO:0000269|PubMed:18508763}.
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 ECO:0000269|PubMed:18508763};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02120,
CC ECO:0000269|PubMed:18508763};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.39 mM for meso-2,6-diaminoheptanedioate
CC {ECO:0000269|PubMed:18508763};
CC Note=kcat is 939 min(-1). {ECO:0000269|PubMed:18508763};
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 ECO:0000305|PubMed:18508763}.
CC -!- MISCELLANEOUS: May adopt an induced-fit catalytic mechanism, in which
CC the active site loop (residues 137-155) cycles through down and up
CC conformations to stabilize catalytic intermediates and release reaction
CC products, respectively. {ECO:0000305|PubMed:18508763}.
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; EU056336; ABW70801.1; -; Genomic_DNA.
DR RefSeq; WP_077231782.1; NZ_AP017633.1.
DR PDB; 2QGH; X-ray; 2.30 A; A=1-405.
DR PDB; 3C5Q; X-ray; 2.40 A; A=1-405.
DR PDBsum; 2QGH; -.
DR PDBsum; 3C5Q; -.
DR AlphaFoldDB; B4XMC6; -.
DR SMR; B4XMC6; -.
DR STRING; 1345592.CBOM010000001_gene166; -.
DR eggNOG; COG0019; Bacteria.
DR UniPathway; UPA00034; UER00027.
DR EvolutionaryTrace; B4XMC6; -.
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.
PE 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; Decarboxylase; Lyase;
KW Lysine biosynthesis; Pyridoxal phosphate.
FT CHAIN 1..405
FT /note="Diaminopimelate decarboxylase"
FT /id="PRO_0000411130"
FT ACT_SITE 329
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 225
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:18508763"
FT BINDING 259..262
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120,
FT ECO:0000269|PubMed:18508763"
FT BINDING 262
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:18508763"
FT BINDING 298
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:18508763"
FT BINDING 302
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:18508763"
FT BINDING 330
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:18508763"
FT BINDING 358
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:18508763"
FT BINDING 358
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:18508763"
FT MOD_RES 46
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000269|PubMed:18508763"
FT MUTAGEN 148
FT /note="I->A: Nearly no change in substrate affinity and 47-
FT fold decrease in catalytic activity."
FT /evidence="ECO:0000269|PubMed:18508763"
FT MUTAGEN 148
FT /note="I->D: 2-fold decrease in substrate affinity and 235-
FT fold decrease in catalytic activity."
FT /evidence="ECO:0000269|PubMed:18508763"
FT MUTAGEN 148
FT /note="I->F: 4-fold increase in substrate affinity and 23-
FT fold decrease in catalytic activity."
FT /evidence="ECO:0000269|PubMed:18508763"
FT MUTAGEN 148
FT /note="I->G: Nearly no change in substrate affinity and
FT 235-fold decrease in catalytic activity."
FT /evidence="ECO:0000269|PubMed:18508763"
FT MUTAGEN 148
FT /note="I->K: Nearly no change in substrate affinity and 55-
FT fold decrease in catalytic activity."
FT /evidence="ECO:0000269|PubMed:18508763"
FT MUTAGEN 148
FT /note="I->L: 13-fold increase in substrate affinity and 40-
FT fold decrease in catalytic activity."
FT /evidence="ECO:0000269|PubMed:18508763"
FT HELIX 4..10
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 13..19
FT /evidence="ECO:0007829|PDB:2QGH"
FT HELIX 20..32
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 39..44
FT /evidence="ECO:0007829|PDB:2QGH"
FT HELIX 45..47
FT /evidence="ECO:0007829|PDB:2QGH"
FT HELIX 51..59
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 63..68
FT /evidence="ECO:0007829|PDB:2QGH"
FT HELIX 69..77
FT /evidence="ECO:0007829|PDB:2QGH"
FT HELIX 82..84
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 85..87
FT /evidence="ECO:0007829|PDB:2QGH"
FT HELIX 94..102
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 106..110
FT /evidence="ECO:0007829|PDB:2QGH"
FT HELIX 113..126
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 130..136
FT /evidence="ECO:0007829|PDB:2QGH"
FT HELIX 146..148
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 155..159
FT /evidence="ECO:0007829|PDB:2QGH"
FT HELIX 161..173
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 175..183
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 187..190
FT /evidence="ECO:0007829|PDB:2QGH"
FT HELIX 193..212
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 219..221
FT /evidence="ECO:0007829|PDB:2QGH"
FT HELIX 238..248
FT /evidence="ECO:0007829|PDB:2QGH"
FT TURN 249..251
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 255..258
FT /evidence="ECO:0007829|PDB:2QGH"
FT HELIX 262..265
FT /evidence="ECO:0007829|PDB:2QGH"
FT TURN 266..268
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 269..279
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 286..290
FT /evidence="ECO:0007829|PDB:2QGH"
FT TURN 293..295
FT /evidence="ECO:0007829|PDB:2QGH"
FT HELIX 298..302
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 308..310
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 320..325
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 327..330
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 334..341
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 349..352
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 356..359
FT /evidence="ECO:0007829|PDB:2QGH"
FT HELIX 360..362
FT /evidence="ECO:0007829|PDB:2QGH"
FT TURN 366..368
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 373..377
FT /evidence="ECO:0007829|PDB:2QGH"
FT STRAND 382..386
FT /evidence="ECO:0007829|PDB:2QGH"
FT HELIX 391..394
FT /evidence="ECO:0007829|PDB:2QGH"
FT HELIX 396..398
FT /evidence="ECO:0007829|PDB:2QGH"
FT TURN 399..401
FT /evidence="ECO:0007829|PDB:2QGH"
SQ SEQUENCE 405 AA; 45242 MW; 5F76BC7A0A635CF2 CRC64;
MFNYEELFQT HKTPFYLYDF DKIKQAFLNY KEAFKGRKSL ICYALKANSN LSILSLLAHL
ESGADCVSIG EIQRALKAGI KPYRIVFSGV GKSAFEIEQA LKLNILFLNV ESFMELKTIE
TIAQSLGIKA RISIRINPNI DAKTHPYIST GLKENKFGVG EKEALEMFLW AKKSAFLEPV
SVHFHIGSQL LDLEPIIEAS QKVAKIAKSL IALGIDLRFF DVGGGIGVSY ENEETIKLYD
YAQGILNALQ GLDLTIICEP GRSIVAESGE LITQVLYEKK AQNKRFVIVD AGMNDFLRPS
LYHAKHAIRV ITPSKGREIS PCDVVGPVCE SSDTFLKDAH LPELEPGDKI AIEKVGAYGS
SMASQYNSRP KLLELALEDH KIRVIRKREA LEDLWRLEEE GLKGV
