dxr: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

dxr

Gene Synonym(s)

ECK0172, b0173, JW0168, ispC, yaeM[1], yaeM

Product Desc.

Dxr[2][3];

Component of DXP reductoisomerase[2]; 1-deoxy-D-xylulose 5-phosphate reductoisomerase[3]

1-deoxy-D-xylulose 5-phosphate (DXP) reductoisomerase, NAPDH-dependent; also called 2-C-methyl-D-erythritol 4-phosphate (MEP) synthase; alternative nonmevalonate (DXP) pathway for terpenoid biosynthesis; dimeric[4]

Product Synonyms(s)

1-deoxy-D-xylulose 5-phosphate reductoisomerase[1], B0173[2][1], Dxr[2][1], YaeM[2][1], IspC[2][1] , ECK0172, ispC, JW0168, yaeM, b0173

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): dxr[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

dxr

Mnemonic

Deoxy-xyulose-P reductoisomerase

Synonyms

ECK0172, b0173, JW0168, ispC, yaeM[1], yaeM

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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

4.17 minutes 

MG1655: 193521..194717
<gbrowseImage> name=NC_000913:193521..194717 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 193520..194716
<gbrowseImage> name=NC_012759:193520..194716 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 193521..194717
<gbrowseImage> name=NC_007779:193521..194717 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 167625..168821
<gbrowseImage> name=NC_010473:167625..168821 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
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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

dxr::aphII

insertion of aphII gene at BalI site in dxr

Auxotrophies

2-C-methylerythritol auxotrophy

PMID:10361694

Defective in the nonmevalonate pathway for isoprenoid synthesis.

aphII was from Tn5 and confers kanamycin resistance

dxrH153Q

H153Q

Increase in KM for substrate. Reduces activity 35-fold

seeded from UniProt:P45568

dxrH209Q

H209Q

Increase in KM for substrate. Reduces activity 5000-fold

seeded from UniProt:P45568

dxrE231K

E231K

No effect on KM for substrate. Reduces activity by over 99.9%

seeded from UniProt:P45568

dxrH257Q

H257Q

Strong increase in KM for substrate. Loss of activity

seeded from UniProt:P45568

dxrG14D

G14D

Loss of solubility and activity

seeded from UniProt:P45568

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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

JW0168

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAGCAACTCACCATTCTGGG

Primer 2:CCGCTTGCGAGACGCATCACCTC

21C8

Kohara Phage

Genobase

PMID:3038334

12D5

Kohara Phage

Genobase

PMID:3038334

E2B8

Kohara Phage

Genobase

PMID:3038334

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[5]

est. P1 cotransduction: 14% [6]

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[5]

est. P1 cotransduction: 20% [6]
Synonyms:zae-502::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:EG12715

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12715

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002371

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945019

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2575

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000592

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

Dxr

Synonyms

1-deoxy-D-xylulose 5-phosphate reductoisomerase[1], B0173[2][1], Dxr[2][1], YaeM[2][1], IspC[2][1] , ECK0172, ispC, JW0168, yaeM, b0173

Product description

Dxr[2][3];

Component of DXP reductoisomerase[2]; 1-deoxy-D-xylulose 5-phosphate reductoisomerase[3]

1-deoxy-D-xylulose 5-phosphate (DXP) reductoisomerase, NAPDH-dependent; also called 2-C-methyl-D-erythritol 4-phosphate (MEP) synthase; alternative nonmevalonate (DXP) pathway for terpenoid biosynthesis; dimeric[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:0005488

binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016040

F

Seeded from EcoCyc (v14.0)

complete

GO:0008299

isoprenoid biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003821

P

Seeded from EcoCyc (v14.0)

complete

GO:0008299

isoprenoid biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013512

P

Seeded from EcoCyc (v14.0)

complete

GO:0008299

isoprenoid biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013644

P

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:0016114

terpenoid biosynthetic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00183

P

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

GO:0030604

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

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00183

F

Seeded from EcoCyc (v14.0)

complete

GO:0030604

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

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003821

F

Seeded from EcoCyc (v14.0)

complete

GO:0030604

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

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013512

F

Seeded from EcoCyc (v14.0)

complete

GO:0030604

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

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013644

F

Seeded from EcoCyc (v14.0)

complete

GO:0030604

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

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.1.1.267

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003821

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013512

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013644

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc (v14.0)

complete

GO:0050897

cobalt ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0170

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003821

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013512

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013644

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

P

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 DXP reductoisomerase

could be indirect

Protein

pflB

PMID:16606699

Experiment(s):EBI-1135787

Protein

groL

PMID:16606699

Experiment(s):EBI-1135787

Protein

ptsP

PMID:16606699

Experiment(s):EBI-1135787

Protein

clpB

PMID:19402753

LCMS(ID Probability):99.3

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.6

Protein

cspE

PMID:19402753

LCMS(ID Probability):99.4

Protein

osmY

PMID:19402753

LCMS(ID Probability):99.6

Protein

sucB

PMID:19402753

LCMS(ID Probability):99.6

Protein

speD

PMID:19402753

LCMS(ID Probability):99.6

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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 

MKQLTILGST GSIGCSTLDV VRHNPEHFRV VALVAGKNVT RMVEQCLEFS PRYAVMDDEA
SAKLLKTMLQ QQGSRTEVLS GQQAACDMAA LEDVDQVMAA IVGAAGLLPT LAAIRAGKTI
LLANKESLVT CGRLFMDAVK QSKAQLLPVD SEHNAIFQSL PQPIQHNLGY ADLEQNGVVS
ILLTGSGGPF RETPLRDLAT MTPDQACRHP NWSMGRKISV DSATMMNKGL EYIEARWLFN
ASASQMEVLI HPQSVIHSMV RYQDGSVLAQ LGEPDMRTPI AHTMAWPNRV NSGVKPLDFC
KLSALTFAAP DYDRYPCLKL AMEAFEQGQA ATTALNAANE ITVAAFLAQQ IRFTDIAALN
LSVLEKMDMR EPQCVDDVLS VDANAREVAR KEVMRLAS
Length

398

Mol. Wt

43.387 kDa

pI

5.9 (calculated)

Extinction coefficient

25,440 - 26,440 (calc based on 6 Y, 3 W, and 8 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

Domain

4..132

PF02670 1-deoxy-D-xylulose 5-phosphate reductoisomerase

PMID:19920124

Domain

146..239

PF08436 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal

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=dxr 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:16128166

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945019

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000592

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P45568

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12715

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12715

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945019

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002371

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2575

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

773

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

122

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

373

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)

dxr

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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_000913:193501..193541 source=MG1655 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:b0173 (EcoliWiki Page)

NCBI GEO profiles for dxr

microarray

GenExpDB:b0173 (EcoliWiki Page)

Summary of data for dxr 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

GFP Fusion

Intergenic region (193332..193584) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ08; Well:C4[7]

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Notes

Accessions Related to dxr Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG12715

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2575

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0173

EcoGene

EcoGene:EG12715

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002371

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000592

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

  • AT5G62790 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q70EZ8 (score: 1.000; bootstrap: 100%)
  • Q9FXZ7 (score: 0.812)
  • Q9FTN0 (score: 0.789)
  • Q8W250 (score: 0.785)

From Inparanoid:20070104

Shigella flexneri

YAEM

From SHIGELLACYC

E. coli O157

YAEM

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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

Database Accession Notes

Pfam (EcoliWiki Page)

PF02670 1-deoxy-D-xylulose 5-phosphate reductoisomerase

Superfamily (EcoliWiki Page)

SUPERFAMILY:51735

Superfamily (EcoliWiki Page)

SUPERFAMILY:55347

Superfamily (EcoliWiki Page)

SUPERFAMILY:69055

Pfam (EcoliWiki Page)

PF08436 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal

EcoCyc

EcoCyc:EG12715

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12715

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002371

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2575

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000592

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 1.12 1.13 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 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).
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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