DCDA_THEMA
ID DCDA_THEMA Reviewed; 386 AA.
AC Q9X1K5;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 137.
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=TM_1517;
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(1999).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH PLP, COFACTOR, AND
RP SUBUNIT.
RG RIKEN structural genomics initiative (RSGI);
RT "Crystal structure analysis of diaminopimelate decarboxylate (LysA).";
RL Submitted (FEB-2009) to the PDB data bank.
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, ECO:0000269|Ref.2};
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|Ref.2}.
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; AE000512; AAD36584.1; -; Genomic_DNA.
DR PIR; F72245; F72245.
DR RefSeq; NP_229317.1; NC_000853.1.
DR RefSeq; WP_004081870.1; NZ_CP011107.1.
DR PDB; 2YXX; X-ray; 1.70 A; A=1-386.
DR PDBsum; 2YXX; -.
DR AlphaFoldDB; Q9X1K5; -.
DR SMR; Q9X1K5; -.
DR STRING; 243274.THEMA_06715; -.
DR EnsemblBacteria; AAD36584; AAD36584; TM_1517.
DR KEGG; tma:TM1517; -.
DR eggNOG; COG0019; Bacteria.
DR InParanoid; Q9X1K5; -.
DR OMA; YCRSMAS; -.
DR OrthoDB; 861683at2; -.
DR UniPathway; UPA00034; UER00027.
DR EvolutionaryTrace; Q9X1K5; -.
DR Proteomes; UP000008183; 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; 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; Reference proteome.
FT CHAIN 1..386
FT /note="Diaminopimelate decarboxylase"
FT /id="PRO_0000149937"
FT ACT_SITE 314
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 214
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120,
FT ECO:0000269|Ref.2"
FT BINDING 246..249
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120,
FT ECO:0000269|Ref.2"
FT BINDING 249
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 285
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 289
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 315
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 343
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120,
FT ECO:0000269|Ref.2"
FT BINDING 343
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"
FT HELIX 3..11
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 13..19
FT /evidence="ECO:0007829|PDB:2YXX"
FT HELIX 20..33
FT /evidence="ECO:0007829|PDB:2YXX"
FT TURN 34..36
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 39..44
FT /evidence="ECO:0007829|PDB:2YXX"
FT HELIX 45..47
FT /evidence="ECO:0007829|PDB:2YXX"
FT HELIX 51..59
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 63..66
FT /evidence="ECO:0007829|PDB:2YXX"
FT HELIX 69..77
FT /evidence="ECO:0007829|PDB:2YXX"
FT HELIX 82..84
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 85..87
FT /evidence="ECO:0007829|PDB:2YXX"
FT HELIX 94..102
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 107..110
FT /evidence="ECO:0007829|PDB:2YXX"
FT HELIX 113..122
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 128..134
FT /evidence="ECO:0007829|PDB:2YXX"
FT TURN 139..141
FT /evidence="ECO:0007829|PDB:2YXX"
FT HELIX 143..151
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 152..157
FT /evidence="ECO:0007829|PDB:2YXX"
FT HELIX 158..160
FT /evidence="ECO:0007829|PDB:2YXX"
FT HELIX 161..168
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 173..177
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 182..184
FT /evidence="ECO:0007829|PDB:2YXX"
FT HELIX 188..204
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 207..210
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 219..221
FT /evidence="ECO:0007829|PDB:2YXX"
FT HELIX 226..232
FT /evidence="ECO:0007829|PDB:2YXX"
FT HELIX 234..237
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 241..247
FT /evidence="ECO:0007829|PDB:2YXX"
FT HELIX 249..252
FT /evidence="ECO:0007829|PDB:2YXX"
FT HELIX 253..255
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 256..268
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 271..277
FT /evidence="ECO:0007829|PDB:2YXX"
FT TURN 280..282
FT /evidence="ECO:0007829|PDB:2YXX"
FT HELIX 285..288
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 295..297
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 304..310
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 312..315
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 319..327
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 334..339
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 341..344
FT /evidence="ECO:0007829|PDB:2YXX"
FT HELIX 345..347
FT /evidence="ECO:0007829|PDB:2YXX"
FT TURN 351..353
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 358..362
FT /evidence="ECO:0007829|PDB:2YXX"
FT STRAND 368..372
FT /evidence="ECO:0007829|PDB:2YXX"
FT HELIX 377..380
FT /evidence="ECO:0007829|PDB:2YXX"
FT TURN 381..383
FT /evidence="ECO:0007829|PDB:2YXX"
SQ SEQUENCE 386 AA; 43982 MW; BB6FD6E9E7869CDB CRC64;
MDILRKVAEI HGTPTYVYFE ETLRKRSRLV KEVFEGVNLL PTFAVKANNN PVLLKILREE
GFGMDVVTKG ELLAAKLAGV PSHTVVWNGN GKSRDQMEHF LREDVRIVNV DSFEEMEIWR
ELNPEGVEYF IRVNPEVDAK THPHISTGLK KHKFGIPLED LDSFMERFRS MNIRGLHVHI
GSQITRVEPF VEAFSKVVRA SERYGFEEIN IGGGWGINYS GEELDLSSYR EKVVPDLKRF
KRVIVEIGRY IVAPSGYLLL RVVLVKRRHN KAFVVVDGGM NVLIRPALYS AYHRIFVLGK
QGKEMRADVV GPLCESGDVI AYDRELPEVE PGDIIAVENA GAYGYTMSNN YNSTTRPAEV
LVRENGRISL IRRRETEMDI FKDVVM
