DCDA_AQUAE
ID DCDA_AQUAE Reviewed; 420 AA.
AC O67262;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 133.
DE RecName: Full=Diaminopimelate decarboxylase;
DE Short=DAP decarboxylase;
DE Short=DAPDC;
DE EC=4.1.1.20;
GN Name=lysA; OrderedLocusNames=aq_1208;
OS Aquifex aeolicus (strain VF5).
OC Bacteria; Aquificae; Aquificales; Aquificaceae; Aquifex.
OX NCBI_TaxID=224324;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=VF5;
RX PubMed=9537320; DOI=10.1038/32831;
RA Deckert G., Warren P.V., Gaasterland T., Young W.G., Lenox A.L.,
RA Graham D.E., Overbeek R., Snead M.A., Keller M., Aujay M., Huber R.,
RA Feldman R.A., Short J.M., Olsen G.J., Swanson R.V.;
RT "The complete genome of the hyperthermophilic bacterium Aquifex aeolicus.";
RL Nature 392:353-358(1998).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.99 ANGSTROMS), AND SUBUNIT.
RG Southeast collaboratory for structural genomics (SECSG);
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: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:0000305|Ref.2}.
CC -!- SIMILARITY: Belongs to the Orn/Lys/Arg decarboxylase class-II family.
CC LysA subfamily. {ECO:0000305}.
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DR EMBL; AE000657; AAC07209.1; -; Genomic_DNA.
DR PIR; C70404; C70404.
DR RefSeq; NP_213826.1; NC_000918.1.
DR RefSeq; WP_010880764.1; NC_000918.1.
DR PDB; 2P3E; X-ray; 1.99 A; A/B=1-420.
DR PDBsum; 2P3E; -.
DR AlphaFoldDB; O67262; -.
DR SMR; O67262; -.
DR STRING; 224324.aq_1208; -.
DR EnsemblBacteria; AAC07209; AAC07209; aq_1208.
DR KEGG; aae:aq_1208; -.
DR PATRIC; fig|224324.8.peg.940; -.
DR eggNOG; COG0019; Bacteria.
DR HOGENOM; CLU_026444_0_0_0; -.
DR InParanoid; O67262; -.
DR OMA; YCRSMAS; -.
DR OrthoDB; 861683at2; -.
DR UniPathway; UPA00034; UER00027.
DR EvolutionaryTrace; O67262; -.
DR Proteomes; UP000000798; 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; IPR022657; De-COase2_CS.
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 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; Decarboxylase; Lyase;
KW Lysine biosynthesis; Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..420
FT /note="Diaminopimelate decarboxylase"
FT /id="PRO_0000149912"
FT ACT_SITE 348
FT /note="Proton donor"
FT /evidence="ECO:0000255"
FT BINDING 244
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 318
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 322
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 349
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 377
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT BINDING 377
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT MOD_RES 65
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250"
FT HELIX 3..7
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 11..14
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 17..20
FT /evidence="ECO:0007829|PDB:2P3E"
FT HELIX 25..32
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 34..40
FT /evidence="ECO:0007829|PDB:2P3E"
FT HELIX 41..54
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 58..63
FT /evidence="ECO:0007829|PDB:2P3E"
FT HELIX 64..66
FT /evidence="ECO:0007829|PDB:2P3E"
FT HELIX 70..78
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 82..87
FT /evidence="ECO:0007829|PDB:2P3E"
FT HELIX 88..96
FT /evidence="ECO:0007829|PDB:2P3E"
FT HELIX 101..103
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 104..106
FT /evidence="ECO:0007829|PDB:2P3E"
FT HELIX 113..121
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 125..129
FT /evidence="ECO:0007829|PDB:2P3E"
FT HELIX 132..145
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 149..156
FT /evidence="ECO:0007829|PDB:2P3E"
FT HELIX 180..182
FT /evidence="ECO:0007829|PDB:2P3E"
FT HELIX 183..191
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 196..202
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 207..211
FT /evidence="ECO:0007829|PDB:2P3E"
FT HELIX 214..231
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 238..240
FT /evidence="ECO:0007829|PDB:2P3E"
FT HELIX 258..265
FT /evidence="ECO:0007829|PDB:2P3E"
FT TURN 266..268
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 274..278
FT /evidence="ECO:0007829|PDB:2P3E"
FT HELIX 282..285
FT /evidence="ECO:0007829|PDB:2P3E"
FT HELIX 286..288
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 289..301
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 304..310
FT /evidence="ECO:0007829|PDB:2P3E"
FT TURN 313..315
FT /evidence="ECO:0007829|PDB:2P3E"
FT HELIX 318..322
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 328..332
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 340..344
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 346..349
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 353..359
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 368..371
FT /evidence="ECO:0007829|PDB:2P3E"
FT TURN 375..378
FT /evidence="ECO:0007829|PDB:2P3E"
FT HELIX 379..381
FT /evidence="ECO:0007829|PDB:2P3E"
FT HELIX 385..387
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 392..397
FT /evidence="ECO:0007829|PDB:2P3E"
FT STRAND 400..405
FT /evidence="ECO:0007829|PDB:2P3E"
FT HELIX 410..414
FT /evidence="ECO:0007829|PDB:2P3E"
FT HELIX 415..417
FT /evidence="ECO:0007829|PDB:2P3E"
SQ SEQUENCE 420 AA; 46966 MW; 4B5E922DBE5338EB CRC64;
MELLKEYNPY LEYRDGELFI EGVSLKELAQ TFGTPLYVYS SNFIKERFEA YRKAFPDALI
CYAVKANFNP HLVKLLGELG AGADIVSGGE LYLAKKAGIP PERIVYAGVG KTEKELTDAV
DSEILMFNVE SRQELDVLNE IAGKLGKKAR IAIRVNPDVD PKTHPYIATG MQKSKFGVDI
REAQKEYEYA SKLENLEIVG IHCHIGSQIL DISPYREAVE KVVSLYESLT QKGFDIKYLD
IGGGLGIKYK PEDKEPAPQD LADLLKDLLE NVKAKIILEP GRSIMGNAGI LITQVQFLKD
KGSKHFIIVD AGMNDLIRPS IYNAYHHIIP VETKERKKVV ADIVGPICET GDFLALDREI
EEVQRGEYLA VLSAGAYGFA MSSHYNMRPR AAEVLVENGS VKLIRKRENY DYIVEPSLDI
