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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei80 – 801Thiamine pyrophosphate1 Publication
Metal bindingi152 – 1521Magnesium1 Publication
Metal bindingi181 – 1811Magnesium1 Publication
Binding sitei181 – 1811Thiamine pyrophosphate1 Publication
Binding sitei288 – 2881Thiamine pyrophosphate1 Publication
Binding sitei370 – 3701Thiamine pyrophosphate1 Publication

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi370 – 3701E → A: Loss of activity. 1 Publication
Mutagenesisi392 – 3921Y → A: Slightly increases activity. 1 Publication
Mutagenesisi392 – 3921Y → F: Increases activity 3-fold. 1 Publication
Mutagenesisi398 – 3981R → A: Loss of activity. 1 Publication
Mutagenesisi431 – 4311H → A: No effect on activity. 1 Publication
Mutagenesisi478 – 4781R → A: Loss of activity. 1 Publication

Chemistry

ChEMBLiCHEMBL3217381.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 6206191-deoxy-D-xylulose-5-phosphate synthasePRO_0000189111Add
BLAST

Proteomic databases

EPDiP77488.
PaxDbiP77488.
PRIDEiP77488.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

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

Chemistry

BindingDBiP77488.

Structurei

Secondary structure

1
620
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni5 – 73Combined sources
Helixi11 – 133Combined sources
Helixi17 – 204Combined sources
Helixi25 – 273Combined sources
Helixi28 – 4215Combined sources
Helixi45 – 473Combined sources
Helixi50 – 545Combined sources
Helixi57 – 6610Combined sources
Turni69 – 713Combined sources
Beta strandi72 – 798Combined sources
Helixi83 – 875Combined sources
Turni88 – 914Combined sources
Helixi92 – 976Combined sources
Turni110 – 1123Combined sources
Beta strandi121 – 1244Combined sources
Helixi126 – 14015Combined sources
Beta strandi146 – 1516Combined sources
Helixi154 – 1563Combined sources
Helixi158 – 17013Combined sources
Beta strandi173 – 1808Combined sources
Helixi240 – 2456Combined sources
Beta strandi249 – 2557Combined sources
Helixi259 – 27113Combined sources
Beta strandi274 – 2818Combined sources
Helixi321 – 33515Combined sources
Beta strandi339 – 3457Combined sources
Turni347 – 3515Combined sources
Helixi353 – 3586Combined sources
Turni360 – 3623Combined sources
Beta strandi363 – 3653Combined sources
Helixi370 – 38213Combined sources
Beta strandi386 – 3927Combined sources
Helixi395 – 3995Combined sources
Helixi400 – 4056Combined sources
Turni406 – 4116Combined sources
Beta strandi415 – 4206Combined sources
Helixi429 – 4313Combined sources
Helixi436 – 4394Combined sources
Turni440 – 4423Combined sources
Beta strandi447 – 4493Combined sources
Helixi454 – 46613Combined sources
Beta strandi472 – 4754Combined sources
Beta strandi478 – 4803Combined sources
Beta strandi498 – 5014Combined sources
Beta strandi504 – 5129Combined sources
Helixi515 – 52511Combined sources
Beta strandi528 – 5314Combined sources
Beta strandi534 – 5374Combined sources
Helixi540 – 54910Combined sources
Beta strandi551 – 56111Combined sources
Helixi565 – 57511Combined sources
Beta strandi582 – 5876Combined sources
Helixi597 – 6037Combined sources
Helixi608 – 61912Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2O1SX-ray2.40A/B/C/D1-620[»]
ProteinModelPortaliP77488.
SMRiP77488. Positions 3-620.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP77488.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni121 – 1233Thiamine pyrophosphate binding
Regioni153 – 1542Thiamine pyrophosphate binding

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

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
EntryMethodResolution (Å)ChainPositionsPDBsum
2O1SX-ray2.40A/B/C/D1-620[»]
ProteinModelPortaliP77488.
SMRiP77488. Positions 3-620.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Chemistry

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

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: September 7, 2016
This is version 148 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.