dxs:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

dxs

Gene Synonym(s)

ECK0414, b0420, JW0410, yajP[1], yajP

Product Desc.

Dxs[2][3];

Component of 1-deoxyxylulose-5-phosphate synthase[3]

DXP synthase; DXP is precursor to isoprenoids, thiamin, pyridoxol[4]

Product Synonyms(s)

1-deoxyxylulose-5-phosphate synthase, thiamine-requiring, FAD-requiring[1], B0420[2][1], YajP[2][1], Dxs[2][1] , ECK0414, JW0410, yajP, b0420

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): xseB-ispA-dxs-yajO[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

dxs

Mnemonic

Deoxy-xylulose-P synthase

Synonyms

ECK0414, b0420, JW0410, yajP[1], yajP

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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

9.43 minutes 

MG1655: 439401..437539
<gbrowseImage> name=NC_000913:437539..439401 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 408599..406737
<gbrowseImage> name=NC_012967:406737..408599 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 340298..342160
<gbrowseImage> name=NC_012759:340298..342160 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 439401..437539
<gbrowseImage> name=NC_007779:437539..439401 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 378732..376870
<gbrowseImage> name=NC_010473:376870..378732 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

437542

Edman degradation

PMID:9371765


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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments
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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW0410

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGTTTTGATATTGCCAAATA

Primer 2:CCTGCCAGCCAGGCCTTGATTTT

19F6

Kohara Phage

Genobase

PMID:3038334

2H5

Kohara Phage

Genobase

PMID:3038334

tsx-247::Tn10

Linked marker

CAG12148 = CGSC7337[5]

est. P1 cotransduction: 82% [6]

zaj-3054::Tn10

Linked marker

CAG12017 = CGSC7339[5]

est. P1 cotransduction: 45% [6]
Synonyms:zba-3054::Tn10

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:G6237

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13612

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002848

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945060

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3378

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001461

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

Dxs

Synonyms

1-deoxyxylulose-5-phosphate synthase, thiamine-requiring, FAD-requiring[1], B0420[2][1], YajP[2][1], Dxs[2][1] , ECK0414, JW0410, yajP, b0420

Product description

Dxs[2][3];

Component of 1-deoxyxylulose-5-phosphate synthase[3]

DXP synthase; DXP is precursor to isoprenoids, thiamin, pyridoxol[4]

EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

GO:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0000287

magnesium ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0460

F

Seeded from EcoCyc (v14.0)

complete

GO:0008299

isoprenoid biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0414

P

Seeded from EcoCyc (v14.0)

complete

GO:0008661

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

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00315

F

Seeded from EcoCyc (v14.0)

complete

GO:0008661

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

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005477

F

Seeded from EcoCyc (v14.0)

complete

GO:0008661

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

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.2.1.7

F

Seeded from EcoCyc (v14.0)

complete

GO:0009228

thiamin biosynthetic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00315

P

Seeded from EcoCyc (v14.0)

complete

GO:0009228

thiamin biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0784

P

Seeded from EcoCyc (v14.0)

complete

GO:0016114

terpenoid biosynthetic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00315

P

Seeded from EcoCyc (v14.0)

complete

GO:0016114

terpenoid biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005477

P

Seeded from EcoCyc (v14.0)

complete

GO:0016624

oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001017

F

Seeded from EcoCyc (v14.0)

complete

GO:0030145

manganese ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0464

F

Seeded from EcoCyc (v14.0)

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

Subunits of 1-deoxyxylulose-5-phosphate synthase

could be indirect

Protein

aceE

PMID:15690043

Experiment(s):EBI-880291

Protein

adhE

PMID:15690043

Experiment(s):EBI-880291

Protein

clpA

PMID:15690043

Experiment(s):EBI-880291

Protein

lon

PMID:15690043

Experiment(s):EBI-880291

Protein

mreB

PMID:15690043

Experiment(s):EBI-880291

Protein

pstB

PMID:15690043

Experiment(s):EBI-880291

Protein

rho

PMID:15690043

Experiment(s):EBI-880291

Protein

tufA

PMID:15690043

Experiment(s):EBI-880291

Protein

yjgL

PMID:15690043

Experiment(s):EBI-880291

Protein

yqeI

PMID:15690043

Experiment(s):EBI-880291

Protein

recA

PMID:15690043

Experiment(s):EBI-880291

Protein

fdnG

PMID:16606699

Experiment(s):EBI-1136539

Protein

appY

PMID:16606699

Experiment(s):EBI-1136539

Protein

gltB

PMID:16606699

Experiment(s):EBI-1136539

Protein

tatE

PMID:16606699

Experiment(s):EBI-1136539

Protein

lacZ

PMID:16606699

Experiment(s):EBI-1136539

Protein

cspA

PMID:16606699

Experiment(s):EBI-1136539

Protein

recA

PMID:19402753

MALDI(Z-score):20.093806

Protein

rho

PMID:19402753

MALDI(Z-score):36.857007

Protein

clpA

PMID:19402753

MALDI(Z-score):23.393679

Protein

pstB

PMID:19402753

MALDI(Z-score):30.495368

Protein

metK

PMID:19402753

MALDI(Z-score):36.974428

Protein

tufB

PMID:19402753

MALDI(Z-score):25.424864

Protein

yqeI

PMID:19402753

MALDI(Z-score):17.053160

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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MSFDIAKYPT LALVDSTQEL RLLPKESLPK LCDELRRYLL DSVSRSSGHF ASGLGTVELT
VALHYVYNTP FDQLIWDVGH QAYPHKILTG RRDKIGTIRQ KGGLHPFPWR GESEYDVLSV
GHSSTSISAG IGIAVAAEKE GKNRRTVCVI GDGAITAGMA FEAMNHAGDI RPDMLVILND
NEMSISENVG ALNNHLAQLL SGKLYSSLRE GGKKVFSGVP PIKELLKRTE EHIKGMVVPG
TLFEELGFNY IGPVDGHDVL GLITTLKNMR DLKGPQFLHI MTKKGRGYEP AEKDPITFHA
VPKFDPSSGC LPKSSGGLPS YSKIFGDWLC ETAAKDNKLM AITPAMREGS GMVEFSRKFP
DRYFDVAIAE QHAVTFAAGL AIGGYKPIVA IYSTFLQRAY DQVLHDVAIQ KLPVLFAIDR
AGIVGADGQT HQGAFDLSYL RCIPEMVIMT PSDENECRQM LYTGYHYNDG PSAVRYPRGN
AVGVELTPLE KLPIGKGIVK RRGEKLAILN FGTLMPEAAK VAESLNATLV DMRFVKPLDE
ALILEMAASH EALVTVEENA IMGGAGSGVN EVLMAHRKPV PVLNIGLPDF FIPQGTQEEM
RAELGLDAAG MEAKIKAWLA
Length

620

Mol. Wt

67.618 kDa

pI

6.6 (calculated)

Extinction coefficient

50,310 - 51,060 (calc based on 19 Y, 4 W, and 6 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Initiator Methionine

1

Removed

UniProt:P77488

Domain

318..482

PF02779 Transketolase, pyrimidine binding domain

PMID:19920124

Domain

495..611

PF02780 Transketolase, C-terminal domain

PMID:19920124

Domain

93..192

PF00676 Dehydrogenase E1 component

PMID:19920124

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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=dxs taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16128405

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945060

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001461

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P77488

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6237

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13612

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945060

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002848

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3378

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

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See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MG1655

752

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

308

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

422

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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Notes

Transcription and Transcriptional Regulation

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<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

xseB-ispA-dxs-yajO

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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:439381..439421 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b0420 (EcoliWiki Page)

NCBI GEO profiles for dxs

microarray

GenExpDB:b0420 (EcoliWiki Page)

Summary of data for dxs from multiple microarray studies

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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes
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Notes

Accessions Related to dxs Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:G6237

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3378

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0420

EcoGene

EcoGene:EG13612

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002848

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001461

Escherichia coli str. K-12 substr. MG1655

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Notes

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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments

Arabidopsis thaliana

  • AT4G15560 (score: 1.000; bootstrap: 100%)
  • AT3G21500 (score: 0.544)
  • AT5G11380 (score: 0.202)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0229442 (score: 1.000; bootstrap: 100%)
  • DDB0230185 (score: 0.245)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA11252-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q6I573 (score: 1.000; bootstrap: 100%)
  • Q5TKB6 (score: 0.993)
  • O22567 (score: 0.728)
  • Q6YU51 (score: 0.566)
  • Q58I00 (score: 0.431)
  • Q58I01 (score: 0.135)
  • Q5VSB8 (score: 0.104)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YBR221C (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPBC30D103c (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

DXS

From SHIGELLACYC

E. coli O157

DXS

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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Database Accession Notes

Pfam (EcoliWiki Page)

PF00676 Dehydrogenase E1 component

Pfam (EcoliWiki Page)

PF02779 Transketolase, pyrimidine binding domain

Pfam (EcoliWiki Page)

PF02780 Transketolase, C-terminal domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:52518

Superfamily (EcoliWiki Page)

SUPERFAMILY:52518

Superfamily (EcoliWiki Page)

SUPERFAMILY:52922

Panther (EcoliWiki Page)

PTHR11624:SF20

EcoCyc

EcoCyc:G6237

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13612

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002848

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3378

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001461

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

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