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Protein

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

Gene

dxs

Organism
Peptoclostridium difficile (strain CD196) (Clostridium difficile)
Status
Unreviewed-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 annotationSAAS annotation

Catalytic activityi

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

Cofactori

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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei74 – 741Thiamine pyrophosphateUniRule annotation
Metal bindingi146 – 1461MagnesiumUniRule annotation
Metal bindingi175 – 1751MagnesiumUniRule annotation
Binding sitei175 – 1751Thiamine pyrophosphateUniRule annotation
Binding sitei287 – 2871Thiamine pyrophosphateUniRule annotation
Binding sitei366 – 3661Thiamine pyrophosphateUniRule annotation

GO - Molecular functioni

  1. 1-deoxy-D-xylulose-5-phosphate synthase activity Source: UniProtKB-HAMAP
  2. magnesium ion binding Source: UniProtKB-HAMAP
  3. thiamine pyrophosphate binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. 1-deoxy-D-xylulose 5-phosphate biosynthetic process Source: UniProtKB-UniPathway
  2. terpenoid biosynthetic process Source: UniProtKB-HAMAP
  3. thiamine biosynthetic process Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

TransferaseUniRule annotationSAAS annotation

Keywords - Biological processi

Isoprene biosynthesisUniRule annotationSAAS annotation, Thiamine biosynthesisUniRule annotationSAAS annotation

Keywords - Ligandi

MagnesiumUniRule annotationSAAS annotation, Metal-bindingUniRule annotationSAAS annotation, Thiamine pyrophosphateUniRule annotationSAAS annotation

Enzyme and pathway databases

BioCyciCDIF645462:GJED-1153-MONOMER.
UniPathwayiUPA00064; UER00091.

Names & Taxonomyi

Protein namesi
Recommended name:
1-deoxy-D-xylulose-5-phosphate synthaseUniRule annotationSAAS annotation (EC:2.2.1.7UniRule annotationSAAS annotation)
Alternative name(s):
1-deoxyxylulose-5-phosphate synthaseUniRule annotation
Gene namesi
Name:dxsUniRule annotationImported
Ordered Locus Names:CD196_1067Imported
OrganismiPeptoclostridium difficile (strain CD196) (Clostridium difficile)Imported
Taxonomic identifieri645462 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesPeptostreptococcaceaePeptoclostridium
ProteomesiUP000002068 Componenti: Chromosome

Interactioni

Subunit structurei

Homodimer.UniRule annotationSAAS annotation

Protein-protein interaction databases

STRINGi645462.CD196_1067.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni115 – 1173Thiamine pyrophosphate bindingUniRule annotation
Regioni147 – 1482Thiamine pyrophosphate bindingUniRule annotation

Sequence similaritiesi

Belongs to the transketolase family. DXPS subfamily.UniRule annotation

Phylogenomic databases

eggNOGiCOG1154.
HOGENOMiHOG000012987.
KOiK01662.
OrthoDBiEOG6BKJ6P.

Family and domain databases

Gene3Di3.40.50.920. 1 hit.
3.40.50.970. 3 hits.
HAMAPiMF_00315. DXP_synth.
InterProiIPR005477. Dxylulose-5-P_synthase.
IPR029061. THDP-binding.
IPR009014. Transketo_C/Pyr-ferredox_oxred.
IPR005475. Transketolase-like_Pyr-bd.
IPR020826. Transketolase_BS.
IPR005476. Transketolase_C.
IPR005474. Transketolase_N.
[Graphical view]
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.

C9XNT4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYKYLDKVNS PKDIKNMSIE EMDLLAKDIR KFLVKSVSKT GGHLASNLGV
60 70 80 90 100
VELTLALHKV FDSPKDKIVW DVGHQSYVHK IVTGRKDCFV SLRQFNGLSG
110 120 130 140 150
FPKENESPHD IFDTGHSSTS ISIATGIACA RDIKKENYSV ISVIGDGSIT
160 170 180 190 200
GGMALEALNQ LGYIDTNMIV ILNDNEMSID KNVGGMSKYL SSIIRNSTVE
210 220 230 240 250
KMTDEVDKIL NVTQTGEILS KTAHRFKDKL MYSFSPQDCS FFDSLGIRYY
260 270 280 290 300
GPIDGHNTKE LIDILRKAKH KKGPVLLHVI TKKGKGYRFA EEQPDKYHGV
310 320 330 340 350
SKFDIKTGVT SAKVKSMSIS VGEKLVDMAN NNEDIVAITA AMPSGTGLNL
360 370 380 390 400
FESAYPKRYY DVGIAEQHAT GFAAGLAKNG MKPYFAVYSS FLQRAYDQVI
410 420 430 440 450
HDVCITKKPV TFLIDRAGLV GNDGETHHGM FDLSYLNSIP NIVVMAPKDT
460 470 480 490 500
REMELMMDLS LKLDCPLAIR YPRGSSYYLD KGEYGEIVLG KYEVLDDGQD
510 520 530 540 550
TVILCIGSMV KHALEAKEIL SREGINPTIV NARFLKPIDE GMLKALLKNH
560 570 580 590 600
KNVVTIEDNI VTGGFGSRIN KFIIDNEYNV NILNIAIPEE FVKHGNIDEL
610 620
YDFVGLSPKS IADKIRKLVI E
Length:621
Mass (Da):68,970
Last modified:November 23, 2009 - v1
Checksum:iB99CF096BFC9762F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FN538970 Genomic DNA. Translation: CBA62029.1.
RefSeqiYP_003214098.1. NC_013315.1.

Genome annotation databases

EnsemblBacteriaiCBA62029; CBA62029; CD196_1067.
KEGGicdc:CD196_1067.
PATRICi19448384. VBICloDif125228_1108.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FN538970 Genomic DNA. Translation: CBA62029.1.
RefSeqiYP_003214098.1. NC_013315.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi645462.CD196_1067.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCBA62029; CBA62029; CD196_1067.
KEGGicdc:CD196_1067.
PATRICi19448384. VBICloDif125228_1108.

Phylogenomic databases

eggNOGiCOG1154.
HOGENOMiHOG000012987.
KOiK01662.
OrthoDBiEOG6BKJ6P.

Enzyme and pathway databases

UniPathwayiUPA00064; UER00091.
BioCyciCDIF645462:GJED-1153-MONOMER.

Family and domain databases

Gene3Di3.40.50.920. 1 hit.
3.40.50.970. 3 hits.
HAMAPiMF_00315. DXP_synth.
InterProiIPR005477. Dxylulose-5-P_synthase.
IPR029061. THDP-binding.
IPR009014. Transketo_C/Pyr-ferredox_oxred.
IPR005475. Transketolase-like_Pyr-bd.
IPR020826. Transketolase_BS.
IPR005476. Transketolase_C.
IPR005474. Transketolase_N.
[Graphical view]
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...

Publicationsi

  1. "Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium."
    Stabler R.A., He M., Dawson L., Martin M., Valiente E., Corton C., Lawley T.D., Sebaihia M., Quail M.A., Rose G., Gerding D.N., Gibert M., Popoff M.R., Parkhill J., Dougan G., Wren B.W.
    Genome Biol. 10:R102.1-R102.15(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CD196Imported.

Entry informationi

Entry nameiC9XNT4_PEPDC
AccessioniPrimary (citable) accession number: C9XNT4
Entry historyi
Integrated into UniProtKB/TrEMBL: November 23, 2009
Last sequence update: November 23, 2009
Last modified: March 31, 2015
This is version 40 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteomeImported

External Data

Dasty 3

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 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.