DCDA_METJA
ID DCDA_METJA Reviewed; 438 AA.
AC Q58497;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 139.
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, ECO:0000269|PubMed:12429091};
GN Name=lysA {ECO:0000255|HAMAP-Rule:MF_02120}; OrderedLocusNames=MJ1097;
OS Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS 10045 / NBRC 100440) (Methanococcus jannaschii).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=243232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT jannaschii.";
RL Science 273:1058-1073(1996).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 5-438 IN COMPLEXES WITH PLP;
RP L-LYSINE AND SUBSTRATE ANALOG, FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
RP ACTIVITY REGULATION, KINETIC PARAMETERS, AND SUBUNIT.
RX PubMed=12429091; DOI=10.1016/s0969-2126(02)00880-8;
RA Ray S.S., Bonanno J.B., Rajashankar K.R., Pinho M.G., He G.,
RA De Lencastre H., Tomasz A., Burley S.K.;
RT "Cocrystal structures of diaminopimelate decarboxylase: mechanism,
RT evolution, and inhibition of an antibiotic resistance accessory factor.";
RL Structure 10:1499-1508(2002).
CC -!- FUNCTION: Specifically catalyzes the decarboxylation of meso-
CC diaminopimelate (meso-DAP) to L-lysine. {ECO:0000269|PubMed:12429091}.
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:0000269|PubMed:12429091};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:12429091};
CC -!- ACTIVITY REGULATION: Competitively inhibited by the substrate analog
CC azelaic acid in vitro but not in vivo. {ECO:0000269|PubMed:12429091}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=588 uM for meso-2,6-diaminoheptanedioate
CC {ECO:0000269|PubMed:12429091};
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:0000305|PubMed:12429091}.
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; L77117; AAB99100.1; -; Genomic_DNA.
DR PIR; H64436; H64436.
DR PDB; 1TUF; X-ray; 2.40 A; A/B=5-438.
DR PDB; 1TWI; X-ray; 2.00 A; A/B/C/D=6-438.
DR PDBsum; 1TUF; -.
DR PDBsum; 1TWI; -.
DR AlphaFoldDB; Q58497; -.
DR SMR; Q58497; -.
DR STRING; 243232.MJ_1097; -.
DR EnsemblBacteria; AAB99100; AAB99100; MJ_1097.
DR KEGG; mja:MJ_1097; -.
DR eggNOG; arCOG02268; Archaea.
DR HOGENOM; CLU_026444_0_1_2; -.
DR InParanoid; Q58497; -.
DR OMA; YCRSMAS; -.
DR PhylomeDB; Q58497; -.
DR SABIO-RK; Q58497; -.
DR UniPathway; UPA00034; UER00027.
DR EvolutionaryTrace; Q58497; -.
DR Proteomes; UP000000805; 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; 2.
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..438
FT /note="Diaminopimelate decarboxylase"
FT /id="PRO_0000149941"
FT ACT_SITE 362
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT BINDING 217
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:12429091"
FT BINDING 254
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:12429091"
FT BINDING 294..297
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120,
FT ECO:0000269|PubMed:12429091"
FT BINDING 297
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:12429091"
FT BINDING 333
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:12429091"
FT BINDING 337
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:12429091"
FT BINDING 363
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:12429091"
FT BINDING 391
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:12429091"
FT BINDING 391
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02120"
FT MOD_RES 73
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000269|PubMed:12429091"
FT STRAND 11..14
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 17..20
FT /evidence="ECO:0007829|PDB:1TWI"
FT HELIX 25..32
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 34..40
FT /evidence="ECO:0007829|PDB:1TWI"
FT HELIX 41..62
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 66..71
FT /evidence="ECO:0007829|PDB:1TWI"
FT HELIX 72..74
FT /evidence="ECO:0007829|PDB:1TWI"
FT HELIX 78..86
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 90..93
FT /evidence="ECO:0007829|PDB:1TWI"
FT HELIX 96..104
FT /evidence="ECO:0007829|PDB:1TWI"
FT HELIX 109..111
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 112..114
FT /evidence="ECO:0007829|PDB:1TWI"
FT HELIX 121..129
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 133..137
FT /evidence="ECO:0007829|PDB:1TWI"
FT HELIX 140..153
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 157..164
FT /evidence="ECO:0007829|PDB:1TWI"
FT TURN 169..171
FT /evidence="ECO:0007829|PDB:1TWI"
FT HELIX 173..181
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 185..188
FT /evidence="ECO:0007829|PDB:1TWI"
FT HELIX 192..202
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 204..212
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 217..219
FT /evidence="ECO:0007829|PDB:1TWI"
FT HELIX 223..241
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 247..250
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 259..263
FT /evidence="ECO:0007829|PDB:1TWI"
FT HELIX 268..280
FT /evidence="ECO:0007829|PDB:1TWI"
FT TURN 281..285
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 290..293
FT /evidence="ECO:0007829|PDB:1TWI"
FT HELIX 297..300
FT /evidence="ECO:0007829|PDB:1TWI"
FT HELIX 301..303
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 304..315
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 320..325
FT /evidence="ECO:0007829|PDB:1TWI"
FT TURN 328..330
FT /evidence="ECO:0007829|PDB:1TWI"
FT HELIX 333..337
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 343..347
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 352..358
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 360..362
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 367..375
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 382..386
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 389..392
FT /evidence="ECO:0007829|PDB:1TWI"
FT HELIX 393..395
FT /evidence="ECO:0007829|PDB:1TWI"
FT TURN 399..401
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 406..411
FT /evidence="ECO:0007829|PDB:1TWI"
FT STRAND 414..419
FT /evidence="ECO:0007829|PDB:1TWI"
FT HELIX 424..427
FT /evidence="ECO:0007829|PDB:1TWI"
FT TURN 428..430
FT /evidence="ECO:0007829|PDB:1TWI"
FT HELIX 435..437
FT /evidence="ECO:0007829|PDB:1TWI"
SQ SEQUENCE 438 AA; 48900 MW; DE031EC50FD57326 CRC64;
MKIMFLGNDT VEIKDGRFFI DGYDAIELAE KFGTPLYVMS EEQIKINYNR YIEAFKRWEE
ETGKEFIVAY AYKANANLAI TRLLAKLGCG ADVVSGGELY IAKLSNVPSK KIVFNGNCKT
KEEIIMGIEA NIRAFNVDSI SELILINETA KELGETANVA FRINPNVNPK THPKISTGLK
KNKFGLDVES GIAMKAIKMA LEMEYVNVVG VHCHIGSQLT DISPFIEETR KVMDFVVELK
EEGIEIEDVN LGGGLGIPYY KDKQIPTQKD LADAIINTML KYKDKVEMPN LILEPGRSLV
ATAGYLLGKV HHIKETPVTK WVMIDAGMND MMRPAMYEAY HHIINCKVKN EKEVVSIAGG
LCESSDVFGR DRELDKVEVG DVLAIFDVGA YGISMANNYN ARGRPRMVLT SKKGVFLIRE
RETYADLIAK DIVPPHLL
