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Protein

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

Gene

dxs

Organism
Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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).UniRule annotation

Catalytic activityi

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

Cofactori

Protein has several cofactor binding sites:
  • Mg2+UniRule annotationNote: Binds 1 Mg2+ ion per subunit.UniRule annotation
  • thiamine diphosphateUniRule annotationNote: Binds 1 thiamine pyrophosphate per subunit.UniRule annotation

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.UniRule annotation
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 sitei70Thiamine pyrophosphateUniRule annotation1
Metal bindingi142MagnesiumUniRule annotation1
Metal bindingi171MagnesiumUniRule annotation1
Binding sitei171Thiamine pyrophosphateUniRule annotation1
Binding sitei278Thiamine pyrophosphateUniRule annotation1
Binding sitei360Thiamine pyrophosphateUniRule annotation1

GO - Molecular functioni

GO - Biological processi

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

BioCyciHPY:HP0354-MONOMER.
UniPathwayiUPA00064; UER00091.

Names & Taxonomyi

Protein namesi
Recommended name:
1-deoxy-D-xylulose-5-phosphate synthaseUniRule annotation (EC:2.2.1.7UniRule annotation)
Alternative name(s):
1-deoxyxylulose-5-phosphate synthaseUniRule annotation
Short name:
DXP synthaseUniRule annotation
Short name:
DXPSUniRule annotation
Gene namesi
Name:dxsUniRule annotation
Ordered Locus Names:HP_0354
OrganismiHelicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Taxonomic identifieri85962 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
Proteomesi
  • UP000000429 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001891191 – 6181-deoxy-D-xylulose-5-phosphate synthaseAdd BLAST618

Proteomic databases

PaxDbiO25121.
PRIDEiO25121.

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

DIPiDIP-3091N.
IntActiO25121. 5 interactors.
MINTiMINT-163092.
STRINGi85962.HP0354.

Structurei

3D structure databases

ProteinModelPortaliO25121.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni111 – 113Thiamine pyrophosphate bindingUniRule annotation3
Regioni143 – 144Thiamine pyrophosphate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the transketolase family. DXPS subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C2V. Bacteria.
COG1154. LUCA.
KOiK01662.
OMAiYKGLCGF.

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.

O25121-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MILQNKTFDL NPNDIAGLEL VCQTLRNRIL EVVSANGGHL SSSLGAVELI
60 70 80 90 100
VGMHALFDCQ KNPFIFDTSH QAYAHKLLTG RFESFSTLRQ FKGLSGFTKP
110 120 130 140 150
SESAYDYFIA GHSSTSVSIG VGVAKAFCLK QALGMPIALL GDGSISAGIF
160 170 180 190 200
YEALNELGDR KYPMIMILND NEMSISTPIG ALSKALSQLM KGPFYQSFRS
210 220 230 240 250
KVKKILSTLP ESVNYLASRF EESFKLITPG VFFEELGINY IGPINGHDLS
260 270 280 290 300
AIIETLKLAK ELKEPVLIHA QTLKGKGYKI AEGRYEKWHG VGPFDLDTGL
310 320 330 340 350
SKKSKSAILS PTEAYSNTLL ELAKKDEKIV GVTAAMPSGT GLDKLIDAYP
360 370 380 390 400
LRFFDVAIAE QHALTSSSAM AKEGFKPFVS IYSTFLQRAY DSIVHDACIS
410 420 430 440 450
SLPIKLAIDR AGIVGEDGET HQGLLDVSYL RSIPNMVIFA PRDNETLKNA
460 470 480 490 500
VRFANEHDSS PCAFRYPRGS FALKEGVFEP SGFVLGQSEL LKKEGEILLI
510 520 530 540 550
GYGNGVGRAH LVQLALKEKN IECALLDLRF LKPLDPNLSA IVAPYQKLYV
560 570 580 590 600
FSDNYKLGGV ASAILEFLSE QNILKPVKSF EIIDEFIMHG NTALVEKSLG
610
LDTESLTDAI LKDLGQER
Length:618
Mass (Da):67,634
Last modified:January 1, 1998 - v1
Checksum:i87334832DAFE3383
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000511 Genomic DNA. Translation: AAD07422.1.
PIRiB64564.
RefSeqiNP_207152.1. NC_000915.1.
WP_000602987.1. NC_000915.1.

Genome annotation databases

EnsemblBacteriaiAAD07422; AAD07422; HP_0354.
GeneIDi898853.
KEGGihpy:HP0354.
PATRICi20591941. VBIHelPyl33062_0367.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000511 Genomic DNA. Translation: AAD07422.1.
PIRiB64564.
RefSeqiNP_207152.1. NC_000915.1.
WP_000602987.1. NC_000915.1.

3D structure databases

ProteinModelPortaliO25121.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-3091N.
IntActiO25121. 5 interactors.
MINTiMINT-163092.
STRINGi85962.HP0354.

Proteomic databases

PaxDbiO25121.
PRIDEiO25121.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD07422; AAD07422; HP_0354.
GeneIDi898853.
KEGGihpy:HP0354.
PATRICi20591941. VBIHelPyl33062_0367.

Phylogenomic databases

eggNOGiENOG4105C2V. Bacteria.
COG1154. LUCA.
KOiK01662.
OMAiYKGLCGF.

Enzyme and pathway databases

UniPathwayiUPA00064; UER00091.
BioCyciHPY:HP0354-MONOMER.

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_HELPY
AccessioniPrimary (citable) accession number: O25121
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 21, 2001
Last sequence update: January 1, 1998
Last modified: October 5, 2016
This is version 112 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Helicobacter pylori
    Helicobacter pylori (strain 26695): entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. 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.