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Protein

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

Gene

dxs

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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).1 Publication

Catalytic activityi

Pyruvate + D-glyceraldehyde 3-phosphate = 1-deoxy-D-xylulose 5-phosphate + CO2.

Cofactori

Protein has several cofactor binding sites:
  • Mg2+1 PublicationNote: Binds 1 Mg2+ ion per subunit.1 Publication
  • thiamine diphosphate1 PublicationNote: Binds 1 thiamine pyrophosphate per subunit.1 Publication

pH dependencei

Optimum pH is 7.5-8.0.

Temperature dependencei

Optimum temperature is 42-44 degrees Celsius.

Pathwayi: 1-deoxy-D-xylulose 5-phosphate biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes 1-deoxy-D-xylulose 5-phosphate from D-glyceraldehyde 3-phosphate and pyruvate.
Proteins known to be involved in this subpathway in this organism are:
  1. 1-deoxy-D-xylulose-5-phosphate synthase (dxs)
This subpathway is part of the pathway 1-deoxy-D-xylulose 5-phosphate biosynthesis, which is itself part of Metabolic intermediate biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 1-deoxy-D-xylulose 5-phosphate from D-glyceraldehyde 3-phosphate and pyruvate, the pathway 1-deoxy-D-xylulose 5-phosphate biosynthesis and in Metabolic intermediate biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei80Thiamine pyrophosphate1 Publication1
Metal bindingi152Magnesium1 Publication1
Metal bindingi181Magnesium1 Publication1
Binding sitei181Thiamine pyrophosphate1 Publication1
Binding sitei288Thiamine pyrophosphate1 Publication1
Binding sitei370Thiamine pyrophosphate1 Publication1

GO - Molecular functioni

  • 1-deoxy-D-xylulose-5-phosphate synthase activity Source: EcoCyc
  • magnesium ion binding Source: UniProtKB-HAMAP
  • thiamine pyrophosphate binding Source: EcoCyc

GO - Biological processi

  • 1-deoxy-D-xylulose 5-phosphate biosynthetic process Source: UniProtKB-UniPathway
  • isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway Source: EcoCyc
  • pyridoxine biosynthetic process Source: EcoCyc
  • terpenoid biosynthetic process Source: UniProtKB-HAMAP
  • thiamine biosynthetic process Source: EcoCyc
  • ubiquinone biosynthetic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Isoprene biosynthesis, Thiamine biosynthesis

Keywords - Ligandi

Magnesium, Metal-binding, Thiamine pyrophosphate

Enzyme and pathway databases

BioCyciEcoCyc:DXS-MONOMER.
ECOL316407:JW0410-MONOMER.
MetaCyc:DXS-MONOMER.
BRENDAi2.2.1.7. 2026.
UniPathwayiUPA00064; UER00091.

Names & Taxonomyi

Protein namesi
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 namesi
Name:dxs
Synonyms:yajP
Ordered Locus Names:b0420, JW0410
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13612. dxs.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi370E → A: Loss of activity. 1 Publication1
Mutagenesisi392Y → A: Slightly increases activity. 1 Publication1
Mutagenesisi392Y → F: Increases activity 3-fold. 1 Publication1
Mutagenesisi398R → A: Loss of activity. 1 Publication1
Mutagenesisi431H → A: No effect on activity. 1 Publication1
Mutagenesisi478R → A: Loss of activity. 1 Publication1

Chemistry databases

ChEMBLiCHEMBL3217381.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001891112 – 6201-deoxy-D-xylulose-5-phosphate synthaseAdd BLAST619

Proteomic databases

EPDiP77488.
PaxDbiP77488.
PRIDEiP77488.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi4259592. 352 interactors.
DIPiDIP-9485N.
IntActiP77488. 18 interactors.
MINTiMINT-1233858.
STRINGi511145.b0420.

Chemistry databases

BindingDBiP77488.

Structurei

Secondary structure

1620
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni5 – 7Combined sources3
Helixi11 – 13Combined sources3
Helixi17 – 20Combined sources4
Helixi25 – 27Combined sources3
Helixi28 – 42Combined sources15
Helixi45 – 47Combined sources3
Helixi50 – 54Combined sources5
Helixi57 – 66Combined sources10
Turni69 – 71Combined sources3
Beta strandi72 – 79Combined sources8
Helixi83 – 87Combined sources5
Turni88 – 91Combined sources4
Helixi92 – 97Combined sources6
Turni110 – 112Combined sources3
Beta strandi121 – 124Combined sources4
Helixi126 – 140Combined sources15
Beta strandi146 – 151Combined sources6
Helixi154 – 156Combined sources3
Helixi158 – 170Combined sources13
Beta strandi173 – 180Combined sources8
Helixi240 – 245Combined sources6
Beta strandi249 – 255Combined sources7
Helixi259 – 271Combined sources13
Beta strandi274 – 281Combined sources8
Helixi321 – 335Combined sources15
Beta strandi339 – 345Combined sources7
Turni347 – 351Combined sources5
Helixi353 – 358Combined sources6
Turni360 – 362Combined sources3
Beta strandi363 – 365Combined sources3
Helixi370 – 382Combined sources13
Beta strandi386 – 392Combined sources7
Helixi395 – 399Combined sources5
Helixi400 – 405Combined sources6
Turni406 – 411Combined sources6
Beta strandi415 – 420Combined sources6
Helixi429 – 431Combined sources3
Helixi436 – 439Combined sources4
Turni440 – 442Combined sources3
Beta strandi447 – 449Combined sources3
Helixi454 – 466Combined sources13
Beta strandi472 – 475Combined sources4
Beta strandi478 – 480Combined sources3
Beta strandi498 – 501Combined sources4
Beta strandi504 – 512Combined sources9
Helixi515 – 525Combined sources11
Beta strandi528 – 531Combined sources4
Beta strandi534 – 537Combined sources4
Helixi540 – 549Combined sources10
Beta strandi551 – 561Combined sources11
Helixi565 – 575Combined sources11
Beta strandi582 – 587Combined sources6
Helixi597 – 603Combined sources7
Helixi608 – 619Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2O1SX-ray2.40A/B/C/D1-620[»]
ProteinModelPortaliP77488.
SMRiP77488.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP77488.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni121 – 123Thiamine pyrophosphate binding3
Regioni153 – 154Thiamine pyrophosphate binding2

Sequence similaritiesi

Belongs to the transketolase family. DXPS subfamily.Curated

Phylogenomic databases

eggNOGiENOG4105C2V. Bacteria.
COG1154. LUCA.
HOGENOMiHOG000012988.
InParanoidiP77488.
KOiK01662.
OMAiYKGLCGF.
PhylomeDBiP77488.

Family and domain databases

CDDicd02007. TPP_DXS. 1 hit.
Gene3Di3.40.50.920. 1 hit.
3.40.50.970. 3 hits.
HAMAPiMF_00315. DXP_synth. 1 hit.
InterProiIPR005477. Dxylulose-5-P_synthase.
IPR029061. THDP-binding.
IPR009014. Transketo_C/PFOR_II.
IPR005475. Transketolase-like_Pyr-bd.
IPR020826. Transketolase_BS.
IPR033248. Transketolase_C.
IPR033247. Transketolase_fam.
IPR005474. Transketolase_N.
[Graphical view]
PANTHERiPTHR11624. PTHR11624. 2 hits.
PfamiPF13292. DXP_synthase_N. 1 hit.
PF02779. Transket_pyr. 1 hit.
PF02780. Transketolase_C. 1 hit.
[Graphical view]
SMARTiSM00861. Transket_pyr. 1 hit.
[Graphical view]
SUPFAMiSSF52518. SSF52518. 3 hits.
SSF52922. SSF52922. 1 hit.
TIGRFAMsiTIGR00204. dxs. 1 hit.
PROSITEiPS00801. TRANSKETOLASE_1. 1 hit.
PS00802. TRANSKETOLASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P77488-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSFDIAKYPT LALVDSTQEL RLLPKESLPK LCDELRRYLL DSVSRSSGHF
60 70 80 90 100
ASGLGTVELT VALHYVYNTP FDQLIWDVGH QAYPHKILTG RRDKIGTIRQ
110 120 130 140 150
KGGLHPFPWR GESEYDVLSV GHSSTSISAG IGIAVAAEKE GKNRRTVCVI
160 170 180 190 200
GDGAITAGMA FEAMNHAGDI RPDMLVILND NEMSISENVG ALNNHLAQLL
210 220 230 240 250
SGKLYSSLRE GGKKVFSGVP PIKELLKRTE EHIKGMVVPG TLFEELGFNY
260 270 280 290 300
IGPVDGHDVL GLITTLKNMR DLKGPQFLHI MTKKGRGYEP AEKDPITFHA
310 320 330 340 350
VPKFDPSSGC LPKSSGGLPS YSKIFGDWLC ETAAKDNKLM AITPAMREGS
360 370 380 390 400
GMVEFSRKFP DRYFDVAIAE QHAVTFAAGL AIGGYKPIVA IYSTFLQRAY
410 420 430 440 450
DQVLHDVAIQ KLPVLFAIDR AGIVGADGQT HQGAFDLSYL RCIPEMVIMT
460 470 480 490 500
PSDENECRQM LYTGYHYNDG PSAVRYPRGN AVGVELTPLE KLPIGKGIVK
510 520 530 540 550
RRGEKLAILN FGTLMPEAAK VAESLNATLV DMRFVKPLDE ALILEMAASH
560 570 580 590 600
EALVTVEENA IMGGAGSGVN EVLMAHRKPV PVLNIGLPDF FIPQGTQEEM
610 620
RAELGLDAAG MEAKIKAWLA
Length:620
Mass (Da):67,617
Last modified:January 23, 2007 - v3
Checksum:iEAF8919809CDF6A1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF035440 Genomic DNA. Translation: AAC46162.1.
U82664 Genomic DNA. Translation: AAB40176.1.
U00096 Genomic DNA. Translation: AAC73523.1.
AP009048 Genomic DNA. Translation: BAE76200.1.
PIRiD64771.
RefSeqiNP_414954.1. NC_000913.3.
WP_000006797.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73523; AAC73523; b0420.
BAE76200; BAE76200; BAE76200.
GeneIDi945060.
KEGGiecj:JW0410.
eco:b0420.
PATRICi32115989. VBIEscCol129921_0436.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF035440 Genomic DNA. Translation: AAC46162.1.
U82664 Genomic DNA. Translation: AAB40176.1.
U00096 Genomic DNA. Translation: AAC73523.1.
AP009048 Genomic DNA. Translation: BAE76200.1.
PIRiD64771.
RefSeqiNP_414954.1. NC_000913.3.
WP_000006797.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2O1SX-ray2.40A/B/C/D1-620[»]
ProteinModelPortaliP77488.
SMRiP77488.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259592. 352 interactors.
DIPiDIP-9485N.
IntActiP77488. 18 interactors.
MINTiMINT-1233858.
STRINGi511145.b0420.

Chemistry databases

BindingDBiP77488.
ChEMBLiCHEMBL3217381.

Proteomic databases

EPDiP77488.
PaxDbiP77488.
PRIDEiP77488.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73523; AAC73523; b0420.
BAE76200; BAE76200; BAE76200.
GeneIDi945060.
KEGGiecj:JW0410.
eco:b0420.
PATRICi32115989. VBIEscCol129921_0436.

Organism-specific databases

EchoBASEiEB3378.
EcoGeneiEG13612. dxs.

Phylogenomic databases

eggNOGiENOG4105C2V. Bacteria.
COG1154. LUCA.
HOGENOMiHOG000012988.
InParanoidiP77488.
KOiK01662.
OMAiYKGLCGF.
PhylomeDBiP77488.

Enzyme and pathway databases

UniPathwayiUPA00064; UER00091.
BioCyciEcoCyc:DXS-MONOMER.
ECOL316407:JW0410-MONOMER.
MetaCyc:DXS-MONOMER.
BRENDAi2.2.1.7. 2026.

Miscellaneous databases

EvolutionaryTraceiP77488.
PROiP77488.

Family and domain databases

CDDicd02007. TPP_DXS. 1 hit.
Gene3Di3.40.50.920. 1 hit.
3.40.50.970. 3 hits.
HAMAPiMF_00315. DXP_synth. 1 hit.
InterProiIPR005477. Dxylulose-5-P_synthase.
IPR029061. THDP-binding.
IPR009014. Transketo_C/PFOR_II.
IPR005475. Transketolase-like_Pyr-bd.
IPR020826. Transketolase_BS.
IPR033248. Transketolase_C.
IPR033247. Transketolase_fam.
IPR005474. Transketolase_N.
[Graphical view]
PANTHERiPTHR11624. PTHR11624. 2 hits.
PfamiPF13292. DXP_synthase_N. 1 hit.
PF02779. Transket_pyr. 1 hit.
PF02780. Transketolase_C. 1 hit.
[Graphical view]
SMARTiSM00861. Transket_pyr. 1 hit.
[Graphical view]
SUPFAMiSSF52518. SSF52518. 3 hits.
SSF52922. SSF52922. 1 hit.
TIGRFAMsiTIGR00204. dxs. 1 hit.
PROSITEiPS00801. TRANSKETOLASE_1. 1 hit.
PS00802. TRANSKETOLASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDXS_ECOLI
AccessioniPrimary (citable) accession number: P77488
Secondary accession number(s): Q2MC06
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 150 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.