DXS_ECOLI
ID DXS_ECOLI Reviewed; 620 AA.
AC P77488; Q2MC06;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 183.
DE RecName: Full=1-deoxy-D-xylulose-5-phosphate synthase {ECO:0000303|PubMed:9371765, ECO:0000305|PubMed:9482846};
DE EC=2.2.1.7 {ECO:0000269|PubMed:9371765, ECO:0000269|PubMed:9482846};
DE AltName: Full=1-deoxyxylulose-5-phosphate synthase {ECO:0000303|PubMed:9371765};
DE Short=DXP synthase {ECO:0000303|PubMed:9371765};
DE Short=DXPS;
GN Name=dxs {ECO:0000303|PubMed:9482846}; Synonyms=yajP;
GN OrderedLocusNames=b0420, JW0410;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND CATALYTIC ACTIVITY.
RC STRAIN=K12;
RX PubMed=9482846; DOI=10.1073/pnas.95.5.2105;
RA Lois L.M., Campos N., Rosa Putra S., Danielsen K., Rohmer M., Boronat A.;
RT "Cloning and characterization of a gene from Escherichia coli encoding a
RT transketolase-like enzyme that catalyzes the synthesis of D-1-deoxyxylulose
RT 5-phosphate, a common precursor for isoprenoid, thiamin, and pyridoxol
RT biosynthesis.";
RL Proc. Natl. Acad. Sci. U.S.A. 95:2105-2110(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT "Sequence of minutes 4-25 of Escherichia coli.";
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP PROTEIN SEQUENCE OF 2-7, FUNCTION, CATALYTIC ACTIVITY, AND COFACTOR.
RX PubMed=9371765; DOI=10.1073/pnas.94.24.12857;
RA Sprenger G.A., Schorken U., Wiegert T., Grolle S., de Graaf A.A.,
RA Taylor S.V., Begley T.P., Bringer-Meyer S., Sahm H.;
RT "Identification of a thiamin-dependent synthase in Escherichia coli
RT required for the formation of the 1-deoxy-D-xylulose 5-phosphate precursor
RT to isoprenoids, thiamin, and pyridoxol.";
RL Proc. Natl. Acad. Sci. U.S.A. 94:12857-12862(1997).
RN [6]
RP CHARACTERIZATION.
RX PubMed=10648511; DOI=10.1128/jb.182.4.891-897.2000;
RA Kuzuyama T., Takagi M., Takahashi S., Seto H.;
RT "Cloning and characterization of 1-deoxy-D-xylulose 5-phosphate synthase
RT from Streptomyces sp. strain CL190, which uses both the mevalonate and
RT nonmevalonate pathways for isopentenyl diphosphate biosynthesis.";
RL J. Bacteriol. 182:891-897(2000).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) IN COMPLEX WITH MAGNESIUM AND
RP THIAMINE PYROPHOSPHATE, FUNCTION, COFACTOR, SUBUNIT, AND MUTAGENESIS OF
RP GLU-370; TYR-392; ARG-398; HIS-431 AND ARG-478.
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:0000269|PubMed:17135236,
CC ECO:0000269|PubMed:9371765, ECO:0000269|PubMed:9482846}.
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; Evidence={ECO:0000269|PubMed:9371765,
CC ECO:0000269|PubMed:9482846};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:12606;
CC Evidence={ECO:0000305|PubMed:9371765, ECO:0000305|PubMed:9482846};
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, ECO:0000269|PubMed:9371765};
CC Note=Binds 1 thiamine pyrophosphate per subunit.
CC {ECO:0000269|PubMed:17135236};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 7.5-8.0.;
CC Temperature dependence:
CC Optimum temperature is 42-44 degrees Celsius.;
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; AF035440; AAC46162.1; -; Genomic_DNA.
DR EMBL; U82664; AAB40176.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73523.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76200.1; -; Genomic_DNA.
DR PIR; D64771; D64771.
DR RefSeq; NP_414954.1; NC_000913.3.
DR RefSeq; WP_000006797.1; NZ_SSZK01000009.1.
DR PDB; 2O1S; X-ray; 2.40 A; A/B/C/D=1-620.
DR PDBsum; 2O1S; -.
DR AlphaFoldDB; P77488; -.
DR SMR; P77488; -.
DR BioGRID; 4259592; 367.
DR DIP; DIP-9485N; -.
DR IntAct; P77488; 19.
DR MINT; P77488; -.
DR STRING; 511145.b0420; -.
DR BindingDB; P77488; -.
DR ChEMBL; CHEMBL3217381; -.
DR jPOST; P77488; -.
DR PaxDb; P77488; -.
DR PRIDE; P77488; -.
DR EnsemblBacteria; AAC73523; AAC73523; b0420.
DR EnsemblBacteria; BAE76200; BAE76200; BAE76200.
DR GeneID; 945060; -.
DR KEGG; ecj:JW0410; -.
DR KEGG; eco:b0420; -.
DR PATRIC; fig|1411691.4.peg.1857; -.
DR EchoBASE; EB3378; -.
DR eggNOG; COG1154; Bacteria.
DR HOGENOM; CLU_009227_1_4_6; -.
DR InParanoid; P77488; -.
DR OMA; QVGYHAQ; -.
DR PhylomeDB; P77488; -.
DR BioCyc; EcoCyc:DXS-MON; -.
DR BioCyc; MetaCyc:DXS-MON; -.
DR BRENDA; 2.2.1.7; 2026.
DR SABIO-RK; P77488; -.
DR UniPathway; UPA00064; UER00091.
DR EvolutionaryTrace; P77488; -.
DR PRO; PR:P77488; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0008661; F:1-deoxy-D-xylulose-5-phosphate synthase activity; IDA:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0030976; F:thiamine pyrophosphate binding; IDA:EcoCyc.
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; IMP:EcoCyc.
DR GO; GO:0008299; P:isoprenoid biosynthetic process; IMP:EcoCyc.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IDA:EcoCyc.
DR GO; GO:0016114; P:terpenoid biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0009228; P:thiamine biosynthetic process; IMP:EcoCyc.
DR GO; GO:0006744; P:ubiquinone biosynthetic process; IDA:EcoCyc.
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 InterPro; IPR005474; Transketolase_N.
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; PS00801; TRANSKETOLASE_1; 1.
DR PROSITE; PS00802; TRANSKETOLASE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Isoprene biosynthesis; Magnesium;
KW Metal-binding; Reference proteome; Thiamine biosynthesis;
KW Thiamine pyrophosphate; Transferase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:9371765"
FT CHAIN 2..620
FT /note="1-deoxy-D-xylulose-5-phosphate synthase"
FT /id="PRO_0000189111"
FT BINDING 80
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000269|PubMed:17135236"
FT BINDING 121..123
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT BINDING 152
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:17135236"
FT BINDING 153..154
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT BINDING 181
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:17135236"
FT BINDING 181
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000269|PubMed:17135236"
FT BINDING 288
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000269|PubMed:17135236"
FT BINDING 370
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000269|PubMed:17135236"
FT MUTAGEN 370
FT /note="E->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:17135236"
FT MUTAGEN 392
FT /note="Y->A: Slightly increases activity."
FT /evidence="ECO:0000269|PubMed:17135236"
FT MUTAGEN 392
FT /note="Y->F: Increases activity 3-fold."
FT /evidence="ECO:0000269|PubMed:17135236"
FT MUTAGEN 398
FT /note="R->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:17135236"
FT MUTAGEN 431
FT /note="H->A: No effect on activity."
FT /evidence="ECO:0000269|PubMed:17135236"
FT MUTAGEN 478
FT /note="R->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:17135236"
FT TURN 5..7
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 11..13
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 17..20
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 25..27
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 28..42
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 45..47
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 50..54
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 57..66
FT /evidence="ECO:0007829|PDB:2O1S"
FT TURN 69..71
FT /evidence="ECO:0007829|PDB:2O1S"
FT STRAND 72..79
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 83..87
FT /evidence="ECO:0007829|PDB:2O1S"
FT TURN 88..91
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 92..97
FT /evidence="ECO:0007829|PDB:2O1S"
FT TURN 110..112
FT /evidence="ECO:0007829|PDB:2O1S"
FT STRAND 121..124
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 126..140
FT /evidence="ECO:0007829|PDB:2O1S"
FT STRAND 146..151
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 154..156
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 158..170
FT /evidence="ECO:0007829|PDB:2O1S"
FT STRAND 173..180
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 240..245
FT /evidence="ECO:0007829|PDB:2O1S"
FT STRAND 249..255
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 259..271
FT /evidence="ECO:0007829|PDB:2O1S"
FT STRAND 274..281
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 321..335
FT /evidence="ECO:0007829|PDB:2O1S"
FT STRAND 339..345
FT /evidence="ECO:0007829|PDB:2O1S"
FT TURN 347..351
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 353..358
FT /evidence="ECO:0007829|PDB:2O1S"
FT TURN 360..362
FT /evidence="ECO:0007829|PDB:2O1S"
FT STRAND 363..365
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 370..382
FT /evidence="ECO:0007829|PDB:2O1S"
FT STRAND 386..392
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 395..399
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 400..405
FT /evidence="ECO:0007829|PDB:2O1S"
FT TURN 406..411
FT /evidence="ECO:0007829|PDB:2O1S"
FT STRAND 415..420
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 429..431
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 436..439
FT /evidence="ECO:0007829|PDB:2O1S"
FT TURN 440..442
FT /evidence="ECO:0007829|PDB:2O1S"
FT STRAND 447..449
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 454..466
FT /evidence="ECO:0007829|PDB:2O1S"
FT STRAND 472..475
FT /evidence="ECO:0007829|PDB:2O1S"
FT STRAND 478..480
FT /evidence="ECO:0007829|PDB:2O1S"
FT STRAND 498..501
FT /evidence="ECO:0007829|PDB:2O1S"
FT STRAND 504..512
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 515..525
FT /evidence="ECO:0007829|PDB:2O1S"
FT STRAND 528..531
FT /evidence="ECO:0007829|PDB:2O1S"
FT STRAND 534..537
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 540..549
FT /evidence="ECO:0007829|PDB:2O1S"
FT STRAND 551..561
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 565..575
FT /evidence="ECO:0007829|PDB:2O1S"
FT STRAND 582..587
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 597..603
FT /evidence="ECO:0007829|PDB:2O1S"
FT HELIX 608..619
FT /evidence="ECO:0007829|PDB:2O1S"
SQ SEQUENCE 620 AA; 67617 MW; EAF8919809CDF6A1 CRC64;
MSFDIAKYPT LALVDSTQEL RLLPKESLPK LCDELRRYLL DSVSRSSGHF ASGLGTVELT
VALHYVYNTP FDQLIWDVGH QAYPHKILTG RRDKIGTIRQ KGGLHPFPWR GESEYDVLSV
GHSSTSISAG IGIAVAAEKE GKNRRTVCVI GDGAITAGMA FEAMNHAGDI RPDMLVILND
NEMSISENVG ALNNHLAQLL SGKLYSSLRE GGKKVFSGVP PIKELLKRTE EHIKGMVVPG
TLFEELGFNY IGPVDGHDVL GLITTLKNMR DLKGPQFLHI MTKKGRGYEP AEKDPITFHA
VPKFDPSSGC LPKSSGGLPS YSKIFGDWLC ETAAKDNKLM AITPAMREGS GMVEFSRKFP
DRYFDVAIAE QHAVTFAAGL AIGGYKPIVA IYSTFLQRAY DQVLHDVAIQ KLPVLFAIDR
AGIVGADGQT HQGAFDLSYL RCIPEMVIMT PSDENECRQM LYTGYHYNDG PSAVRYPRGN
AVGVELTPLE KLPIGKGIVK RRGEKLAILN FGTLMPEAAK VAESLNATLV DMRFVKPLDE
ALILEMAASH EALVTVEENA IMGGAGSGVN EVLMAHRKPV PVLNIGLPDF FIPQGTQEEM
RAELGLDAAG MEAKIKAWLA
