DXS_DEIRA
ID DXS_DEIRA Reviewed; 629 AA.
AC Q9RUB5;
DT 21-FEB-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=1-deoxy-D-xylulose-5-phosphate synthase;
DE EC=2.2.1.7;
DE AltName: Full=1-deoxyxylulose-5-phosphate synthase;
DE Short=DXP synthase;
DE Short=DXPS;
GN Name=dxs; OrderedLocusNames=DR_1475;
OS Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG
OS 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422).
OC Bacteria; Deinococcus-Thermus; Deinococci; Deinococcales; Deinococcaceae;
OC Deinococcus.
OX NCBI_TaxID=243230;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=10567266; DOI=10.1126/science.286.5444.1571;
RA White O., Eisen J.A., Heidelberg J.F., Hickey E.K., Peterson J.D.,
RA Dodson R.J., Haft D.H., Gwinn M.L., Nelson W.C., Richardson D.L.,
RA Moffat K.S., Qin H., Jiang L., Pamphile W., Crosby M., Shen M.,
RA Vamathevan J.J., Lam P., McDonald L.A., Utterback T.R., Zalewski C.,
RA Makarova K.S., Aravind L., Daly M.J., Minton K.W., Fleischmann R.D.,
RA Ketchum K.A., Nelson K.E., Salzberg S.L., Smith H.O., Venter J.C.,
RA Fraser C.M.;
RT "Genome sequence of the radioresistant bacterium Deinococcus radiodurans
RT R1.";
RL Science 286:1571-1577(1999).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.90 ANGSTROMS) IN COMPLEX WITH MAGNESIUM AND
RP THIAMINE PYROPHOSPHATE, COFACTOR, AND SUBUNIT.
RX PubMed=17135236; DOI=10.1074/jbc.m610235200;
RA Xiang S., Usunow G., Lange G., Busch M., Tong L.;
RT "Crystal structure of 1-deoxy-D-xylulose 5-phosphate synthase, a crucial
RT enzyme for isoprenoids biosynthesis.";
RL J. Biol. Chem. 282:2676-2682(2007).
CC -!- FUNCTION: Catalyzes the acyloin condensation reaction between C atoms 2
CC and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-
CC xylulose-5-phosphate (DXP). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-glyceraldehyde 3-phosphate + H(+) + pyruvate = 1-deoxy-D-
CC xylulose 5-phosphate + CO2; Xref=Rhea:RHEA:12605, ChEBI:CHEBI:15361,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:57792,
CC ChEBI:CHEBI:59776; EC=2.2.1.7;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:17135236};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000269|PubMed:17135236};
CC -!- COFACTOR:
CC Name=thiamine diphosphate; Xref=ChEBI:CHEBI:58937;
CC Evidence={ECO:0000269|PubMed:17135236};
CC Note=Binds 1 thiamine pyrophosphate per subunit.
CC {ECO:0000269|PubMed:17135236};
CC -!- PATHWAY: Metabolic intermediate biosynthesis; 1-deoxy-D-xylulose 5-
CC phosphate biosynthesis; 1-deoxy-D-xylulose 5-phosphate from D-
CC glyceraldehyde 3-phosphate and pyruvate: step 1/1.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:17135236}.
CC -!- SIMILARITY: Belongs to the transketolase family. DXPS subfamily.
CC {ECO:0000305}.
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DR EMBL; AE000513; AAF11042.1; -; Genomic_DNA.
DR PIR; G75390; G75390.
DR RefSeq; NP_295198.1; NC_001263.1.
DR RefSeq; WP_010888114.1; NZ_CP015081.1.
DR PDB; 2O1X; X-ray; 2.90 A; A/B/C/D=1-629.
DR PDB; 6OUV; X-ray; 1.94 A; A/B=1-629.
DR PDB; 6OUW; X-ray; 2.40 A; A=1-629.
DR PDB; 6XXG; X-ray; 2.10 A; AAA/BBB=2-199, AAA/BBB=244-629.
DR PDBsum; 2O1X; -.
DR PDBsum; 6OUV; -.
DR PDBsum; 6OUW; -.
DR PDBsum; 6XXG; -.
DR AlphaFoldDB; Q9RUB5; -.
DR SMR; Q9RUB5; -.
DR STRING; 243230.DR_1475; -.
DR BindingDB; Q9RUB5; -.
DR ChEMBL; CHEMBL3559650; -.
DR PRIDE; Q9RUB5; -.
DR EnsemblBacteria; AAF11042; AAF11042; DR_1475.
DR KEGG; dra:DR_1475; -.
DR PATRIC; fig|243230.17.peg.1675; -.
DR eggNOG; COG1154; Bacteria.
DR HOGENOM; CLU_009227_1_4_0; -.
DR InParanoid; Q9RUB5; -.
DR OMA; QVGYHAQ; -.
DR OrthoDB; 566385at2; -.
DR BRENDA; 2.2.1.7; 1856.
DR UniPathway; UPA00064; UER00091.
DR EvolutionaryTrace; Q9RUB5; -.
DR Proteomes; UP000002524; Chromosome I.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0008661; F:1-deoxy-D-xylulose-5-phosphate synthase activity; IBA:GO_Central.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0030976; F:thiamine pyrophosphate binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016744; F:transketolase or transaldolase activity; IBA:GO_Central.
DR GO; GO:0052865; P:1-deoxy-D-xylulose 5-phosphate biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0019288; P:isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway; IBA:GO_Central.
DR GO; GO:0016114; P:terpenoid biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0009228; P:thiamine biosynthetic process; IEA:UniProtKB-UniRule.
DR CDD; cd02007; TPP_DXS; 1.
DR Gene3D; 3.40.50.920; -; 1.
DR HAMAP; MF_00315; DXP_synth; 1.
DR InterPro; IPR005477; Dxylulose-5-P_synthase.
DR InterPro; IPR029061; THDP-binding.
DR InterPro; IPR009014; Transketo_C/PFOR_II.
DR InterPro; IPR005475; Transketolase-like_Pyr-bd.
DR InterPro; IPR020826; Transketolase_BS.
DR InterPro; IPR033248; Transketolase_C.
DR PANTHER; PTHR43322; PTHR43322; 1.
DR Pfam; PF13292; DXP_synthase_N; 1.
DR Pfam; PF02779; Transket_pyr; 1.
DR Pfam; PF02780; Transketolase_C; 1.
DR SMART; SM00861; Transket_pyr; 1.
DR SUPFAM; SSF52518; SSF52518; 2.
DR SUPFAM; SSF52922; SSF52922; 1.
DR TIGRFAMs; TIGR00204; dxs; 1.
DR PROSITE; PS00802; TRANSKETOLASE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Isoprene biosynthesis; Magnesium; Metal-binding;
KW Reference proteome; Thiamine biosynthesis; Thiamine pyrophosphate;
KW Transferase.
FT CHAIN 1..629
FT /note="1-deoxy-D-xylulose-5-phosphate synthase"
FT /id="PRO_0000189110"
FT BINDING 82
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000269|PubMed:17135236"
FT BINDING 123..125
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT BINDING 154
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:17135236"
FT BINDING 155..156
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT BINDING 183
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:17135236"
FT BINDING 183
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000269|PubMed:17135236"
FT BINDING 373
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000269|PubMed:17135236"
FT HELIX 13..15
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 19..23
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 27..29
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 30..45
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 48..50
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 52..57
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 59..68
FT /evidence="ECO:0007829|PDB:6OUV"
FT TURN 71..73
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 74..81
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 85..89
FT /evidence="ECO:0007829|PDB:6OUV"
FT TURN 90..92
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 95..99
FT /evidence="ECO:0007829|PDB:6OUV"
FT TURN 112..114
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 123..126
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 128..141
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 148..153
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 156..158
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 160..172
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 175..182
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 184..189
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 193..199
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 218..222
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 249..251
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 254..260
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 264..272
FT /evidence="ECO:0007829|PDB:6OUV"
FT TURN 273..276
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 277..286
FT /evidence="ECO:0007829|PDB:6OUV"
FT TURN 289..292
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 294..298
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 302..304
FT /evidence="ECO:0007829|PDB:6OUV"
FT TURN 311..313
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 324..338
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 342..348
FT /evidence="ECO:0007829|PDB:6OUV"
FT TURN 350..354
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 356..361
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 363..365
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 366..368
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 373..385
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 389..395
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 396..399
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 400..402
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 403..409
FT /evidence="ECO:0007829|PDB:6OUV"
FT TURN 410..414
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 418..425
FT /evidence="ECO:0007829|PDB:6OUV"
FT TURN 432..434
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 439..442
FT /evidence="ECO:0007829|PDB:6OUV"
FT TURN 443..445
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 450..452
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 457..469
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 470..472
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 474..477
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 480..482
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 500..503
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 506..512
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 514..523
FT /evidence="ECO:0007829|PDB:6OUV"
FT TURN 524..526
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 530..534
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 537..540
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 543..552
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 554..567
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 568..578
FT /evidence="ECO:0007829|PDB:6OUV"
FT STRAND 584..590
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 600..607
FT /evidence="ECO:0007829|PDB:6OUV"
FT HELIX 611..620
FT /evidence="ECO:0007829|PDB:6OUV"
SQ SEQUENCE 629 AA; 67645 MW; 1B73A37BBB8E4870 CRC64;
MNELPGTSDT PLLDQIHGPK DLKRLSREQL PALTEELRGE IVRVCSRGGL HLASSLGAVD
IITALHYVLD SPRDRILFDV GHQAYAHKIL TGRRDQMADI KKEGGISGFT KVSESEHDAI
TVGHASTSLA NALGMALARD AQGKDFHVAA VIGDGSLTGG MALAALNTIG DMGRKMLIVL
NDNEMSISEN VGAMNKFMRG LQVQKWFQEG EGAGKKAVEA VSKPLADFMS RAKNSTRHFF
DPASVNPFAA MGVRYVGPVD GHNVQELVWL LERLVDLDGP TILHIVTTKG KGLSYAEADP
IYWHGPAKFD PATGEYVPSS AYSWSAAFGE AVTEWAKTDP RTFVVTPAMR EGSGLVEFSR
VHPHRYLDVG IAEEVAVTTA AGMALQGMRP VVAIYSTFLQ RAYDQVLHDV AIEHLNVTFC
IDRAGIVGAD GATHNGVFDL SFLRSIPGVR IGLPKDAAEL RGMLKYAQTH DGPFAIRYPR
GNTAQVPAGT WPDLKWGEWE RLKGGDDVVI LAGGKALDYA LKAAEDLPGV GVVNARFVKP
LDEEMLREVG GRARALITVE DNTVVGGFGG AVLEALNSMN LHPTVRVLGI PDEFQEHATA
ESVHARAGID APAIRTVLAE LGVDVPIEV
