Reviewed, UniProtKB/Swiss-Prot P77488 (DXS_ECOLI)

Names and origin

Protein names

Recommended name:
    1-deoxy-D-xylulose-5-phosphate synthase
    EC=2.2.1.7
Alternative name(s):
    1-deoxyxylulose-5-phosphate synthase
      Short name=DXP synthase
      Short name=DXPS

Gene names

Name:	dxs
Synonyms:	yajP
Ordered Locus Names:	b0420, JW0410

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	620 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP). HAMAP MF_00315
Catalytic activity	Pyruvate + D-glyceraldehyde 3-phosphate = 1-deoxy-D-xylulose 5-phosphate + CO2. HAMAP MF_00315
Cofactor	Binds 1 thiamine pyrophosphate per subunit By similarity.
Pathway	Metabolic intermediate biosynthesis; 1-deoxy-D-xylulose 5-phosphate biosynthesis; 1-deoxy-D-xylulose 5-phosphate from D-glyceraldehyde 3-phosphate and pyruvate: step 1/1. HAMAP MF_00315
Subunit structure	Homodimer. HAMAP MF_00315
Sequence similarities	Belongs to the transketolase family. DXPS subfamily.
Biophysicochemical properties	pH dependence: Optimum pH is 7.5-8.0. HAMAP MF_00315 Temperature dependence: Optimum temperature is 42-44 degrees Celsius.

Ontologies

Keywords
Biological process	Isoprene biosynthesis Thiamine biosynthesis
Ligand	Magnesium Manganese Thiamine pyrophosphate
Molecular function	Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	terpenoid biosynthetic process Inferred from electronic annotation. Source: HAMAP thiamin biosynthetic process Inferred from electronic annotation. Source: HAMAP
Molecular function	1-deoxy-D-xylulose-5-phosphate synthase activity Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW manganese ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.5

Chain

2 – 620

619

1-deoxy-D-xylulose-5-phosphate synthase HAMAP MF_00315

PRO_0000189111

Secondary structure

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620

Helix Strand Turn

Details...

Turn

5 – 7

3

Helix

11 – 13

3

Helix

17 – 20

4

Helix

25 – 27

3

Helix

28 – 42

15

Helix

45 – 47

3

Helix

50 – 54

5

Helix

57 – 66

10

Turn

69 – 71

3

Beta strand

72 – 79

8

Helix

83 – 87

5

Turn

88 – 91

4

Helix

92 – 97

6

Turn

110 – 112

3

Beta strand

121 – 124

4

Helix

126 – 140

15

Beta strand

146 – 151

6

Helix

154 – 156

3

Helix

158 – 170

13

Beta strand

173 – 180

8

Helix

240 – 245

6

Beta strand

249 – 255

7

Helix

259 – 271

13

Beta strand

274 – 281

8

Helix

321 – 335

15

Beta strand

339 – 345

7

Turn

347 – 351

5

Helix

353 – 358

6

Turn

360 – 362

3

Beta strand

363 – 365

3

Helix

370 – 382

13

Beta strand

386 – 392

7

Helix

395 – 399

5

Helix

400 – 405

6

Turn

406 – 411

6

Beta strand

415 – 420

6

Helix

429 – 431

3

Helix

436 – 439

4

Turn

440 – 442

3

Beta strand

447 – 449

3

Helix

454 – 466

13

Beta strand

472 – 475

4

Beta strand

478 – 480

3

Beta strand

498 – 501

4

Beta strand

504 – 512

9

Helix

515 – 525

11

Beta strand

528 – 531

4

Beta strand

534 – 537

4

Helix

540 – 549

10

Beta strand

551 – 561

11

Helix

565 – 575

11

Beta strand

582 – 587

6

Helix

597 – 603

7

Helix

608 – 619

12

Sequences

	Sequence		Length	Mass (Da)
	P77488-1 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: EAF8919809CDF6A1	FASTA	620	67,617
	10 20 30 40 50 60 MSFDIAKYPT LALVDSTQEL RLLPKESLPK LCDELRRYLL DSVSRSSGHF ASGLGTVELT 70 80 90 100 110 120 VALHYVYNTP FDQLIWDVGH QAYPHKILTG RRDKIGTIRQ KGGLHPFPWR GESEYDVLSV 130 140 150 160 170 180 GHSSTSISAG IGIAVAAEKE GKNRRTVCVI GDGAITAGMA FEAMNHAGDI RPDMLVILND 190 200 210 220 230 240 NEMSISENVG ALNNHLAQLL SGKLYSSLRE GGKKVFSGVP PIKELLKRTE EHIKGMVVPG 250 260 270 280 290 300 TLFEELGFNY IGPVDGHDVL GLITTLKNMR DLKGPQFLHI MTKKGRGYEP AEKDPITFHA 310 320 330 340 350 360 VPKFDPSSGC LPKSSGGLPS YSKIFGDWLC ETAAKDNKLM AITPAMREGS GMVEFSRKFP 370 380 390 400 410 420 DRYFDVAIAE QHAVTFAAGL AIGGYKPIVA IYSTFLQRAY DQVLHDVAIQ KLPVLFAIDR 430 440 450 460 470 480 AGIVGADGQT HQGAFDLSYL RCIPEMVIMT PSDENECRQM LYTGYHYNDG PSAVRYPRGN 490 500 510 520 530 540 AVGVELTPLE KLPIGKGIVK RRGEKLAILN FGTLMPEAAK VAESLNATLV DMRFVKPLDE 550 560 570 580 590 600 ALILEMAASH EALVTVEENA IMGGAGSGVN EVLMAHRKPV PVLNIGLPDF FIPQGTQEEM 610 620 RAELGLDAAG MEAKIKAWLA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and characterization of a gene from Escherichia coli encoding a transketolase-like enzyme that catalyzes the synthesis of D-1-deoxyxylulose 5-phosphate, a common precursor for isoprenoid, thiamin, and pyridoxol biosynthesis." Lois L.M., Campos N., Rosa Putra S., Danielsen K., Rohmer M., Boronat A. Proc. Natl. Acad. Sci. U.S.A. 95:2105-2110(1998) [PubMed: 9482846] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION. Strain: K12.
[2]	"Sequence of minutes 4-25 of Escherichia coli." Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W. Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Identification of a thiamin-dependent synthase in Escherichia coli required for the formation of the 1-deoxy-D-xylulose 5-phosphate precursor to isoprenoids, thiamin, and pyridoxol." Sprenger G.A., Schorken U., Wiegert T., Grolle S., de Graaf A.A., Taylor S.V., Begley T.P., Bringer-Meyer S., Sahm H. Proc. Natl. Acad. Sci. U.S.A. 94:12857-12862(1997) [PubMed: 9371765] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-7, CHARACTERIZATION.
[6]	"Cloning and characterization of 1-deoxy-D-xylulose 5-phosphate synthase from Streptomyces sp. strain CL190, which uses both the mevalonate and nonmevalonate pathways for isopentenyl diphosphate biosynthesis." Kuzuyama T., Takagi M., Takahashi S., Seto H. J. Bacteriol. 182:891-897(2000) [PubMed: 10648511] [Abstract] Cited for: CHARACTERIZATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AF035440 Genomic DNA. Translation: AAC46162.1.
U82664 Genomic DNA. Translation: AAB40176.1.
U00096 Genomic DNA. Translation: AAC73523.1.
AP009048 Genomic DNA. Translation: BAE76200.1.

PIR

D64771.

RefSeq

AP_001070.1.
NP_414954.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2O1S	X-ray	2.40	A/B/C/D	1-620	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:9485N.

STRING

P77488.

Proteomic databases

PRIDE

P77488.

Genome annotation databases

GeneID

945060.

GenomeReviews

Gene locus JW0410 in contig AP009048_GR.
Gene locus b0420 in contig U00096_GR.

KEGG

ecj:JW0410.
eco:b0420.

Organism-specific databases

EchoBASE

EB3378.

EcoGene

EG13612. dxs.

CMR

Search...

Phylogenomic databases

HOGENOM

P77488.

OMA

QRFPDRY.

Enzyme and pathway databases

BioCyc

EcoCyc:DXS-MON.
MetaCyc:DXS-MON.

Gene expression databases

Genevestigator

P77488.

Family and domain databases

HAMAP

MF_00315.
[Tree]

InterPro

IPR005477. Dxylulose-5-P_synthase.
IPR015941. Transketolase-like_C.
IPR005475. Transketolase-like_Pyr-bd.
IPR005476. Transketolase_C.
IPR005474. Transketolase_N.
[Graphical view]

Gene3D

G3DSA:3.40.50.920. Transketo_C_like. 1 hit.

Pfam

PF02779. Transket_pyr. 1 hit.
PF02780. Transketolase_C. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00204. dxs. 1 hit.

PROSITE

PS00801. TRANSKETOLASE_1. 1 hit.
PS00802. TRANSKETOLASE_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

DXS_ECOLI

Accession

Primary (citable) accession number: P77488
Secondary accession number(s): Q2MC06

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	January 23, 2007
Last modified:	November 3, 2009
This is version 91 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)