nrdE: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

nrdE

Gene Synonym(s)

ECK2669, b2675, JW2650[1], JW2650

Product Desc.

NrdE[2][3];

Component of ribonucleoside-diphosphate reductase 2, α subunit dimer[2][3]; ribonucleoside-diphosphate reductase 2[2][3]

Product Synonyms(s)

ribonucleoside-diphosphate reductase 2, alpha subunit[1], B2675[2][1], NrdE[2][1] , ECK2669, JW2650, b2675

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): nrdHIEF[2], nrdEF

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

nrdE

Mnemonic

Nucleotide reductase

Synonyms

ECK2669, b2675, JW2650[1], JW2650

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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

60.34 minutes 

MG1655: 2799370..2801514
<gbrowseImage> name=NC_000913:2799370..2801514 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2696100..2698244
<gbrowseImage> name=NC_012967:2696100..2698244 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2685182..2687326
<gbrowseImage> name=NC_012759:2685182..2687326 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2800004..2802148
<gbrowseImage> name=NC_007779:2800004..2802148 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2891135..2893279
<gbrowseImage> name=NC_010473:2891135..2893279 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

ΔnrdE (Keio:JW2650)

deletion

deletion

PMID:16738554

Shigen
CGSC10089[4]

nrdE::Tn5KAN-I-SceI (FB20875)

Insertion at nt 339 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20875

does not contain pKD46

nrdE::Tn5KAN-I-SceI (FB20876)

Insertion at nt 339 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20876

contains pKD46

ΔnrdE756::kan

PMID:16738554

CGSC:102106


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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

JW2650

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCAACGACAACCGCAGAATG

Primer 2:CCAAGTGCACAGGAGACGCAGCC

10H9

Kohara Phage

Genobase

PMID:3038334

8G10

Kohara Phage

Genobase

PMID:3038334

pheA18::Tn10

Linked marker

CAG12158 = CGSC7421[4]

est. P1 cotransduction: 4% [5]

srlD3131::Tn10

Linked marker

CAG18642 = CGSC7423[4]

est. P1 cotransduction: 37% [5]
Synonyms:zfh-3131::Tn10, zfi-3131::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:EG20257

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG20257

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002450

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947155

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4158

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008806

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

NrdE

Synonyms

ribonucleoside-diphosphate reductase 2, alpha subunit[1], B2675[2][1], NrdE[2][1] , ECK2669, JW2650, b2675

Product description

NrdE[2][3];

Component of ribonucleoside-diphosphate reductase 2, α subunit dimer[2][3]; ribonucleoside-diphosphate reductase 2[2][3]

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

PMID:7809142

ISA: Inferred from Sequence Alignment

UniProtKB:Q08698

C

complete

GO:0015949

nucleobase, nucleoside and nucleotide interconversion

PMID:7809142

IGI: Inferred from Genetic Interaction

EcoliWiki:nrdA|EcoliWiki:nrdB

P

A plasmid expressing nrdEFHI genes from Salmonella was capable of complementing nrdAB- mutations in E. coli.

complete

GO:0005524

ATP binding

GO:0016959

ISA: Inferred from Sequence Alignment

UniProtKB:Q08698

F

complete

Contributes to

GO:0004748

ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor

PMID:7809142

IGI: Inferred from Genetic Interaction

EcoliWiki:nrdA|EcoliWiki


F

A plasmid expressing nrdEFHI genes from Salmonella was capable of complementing nrdAB- mutations in E. coli.

new GO replaces obsolete GO:0016959

complete

Contributes to

GO:0004748

ribonucleoside-diphosphate reductase activity

PMID:7809142

IGI: Inferred from Genetic Interaction

EcoliWiki:nrdA|EcoliWiki:nrdB

F

complete

GO:0005971

ribonucleoside-diphosphate reductase complex

PMID:7809142

IGI: Inferred from Genetic Interaction

EcoliWiki:nrdA|EcoliWiki:nrdB

C

complete

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0004748

ribonucleoside-diphosphate reductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000788

F

Seeded from EcoCyc (v14.0)

complete

GO:0009263

deoxyribonucleotide biosynthetic process

PMID:7809142

IGI: Inferred from Genetic Interaction

EcoliWiki:nrdA|EcoliWiki:nrdB

P

complete

GO:0004748

ribonucleoside-diphosphate reductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008926

F

Seeded from EcoCyc (v14.0)

complete

GO:0004748

ribonucleoside-diphosphate reductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013509

F

Seeded from EcoCyc (v14.0)

complete

GO:0004748

ribonucleoside-diphosphate reductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013554

F

Seeded from EcoCyc (v14.0)

complete

GO:0004748

ribonucleoside-diphosphate reductase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.17.4.1

F

Seeded from EcoCyc (v14.0)

complete

GO:0005515

protein binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008926

F

Seeded from EcoCyc (v14.0)

complete

GO:0005515

protein binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013554

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013509

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0005971

ribonucleoside-diphosphate reductase complex

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000788

C

Seeded from EcoCyc (v14.0)

complete

GO:0005971

ribonucleoside-diphosphate reductase complex

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008926

C

Seeded from EcoCyc (v14.0)

complete

GO:0005971

ribonucleoside-diphosphate reductase complex

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013346

C

Seeded from EcoCyc (v14.0)

complete

GO:0005971

ribonucleoside-diphosphate reductase complex

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013554

C

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000788

P

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008926

P

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013509

P

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013554

P

Seeded from EcoCyc (v14.0)

complete

GO:0006260

DNA replication

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0235

P

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008926

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013346

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013509

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013554

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 ribonucleoside-diphosphate reductase 2, α subunit dimer

could be indirect

Protein

intS

PMID:16606699

Experiment(s):EBI-1143641

Protein

tusE

PMID:16606699

Experiment(s):EBI-1143641

Protein

groL

PMID:16606699

Experiment(s):EBI-1143641

Protein

yagA

PMID:16606699

Experiment(s):EBI-1143641

Protein

ygeV

PMID:16606699

Experiment(s):EBI-1143641

Protein

ydcS

PMID:16606699

Experiment(s):EBI-1143641

Protein

ytfM

PMID:16606699

Experiment(s):EBI-1143641

Protein

rplB

PMID:16606699

Experiment(s):EBI-1143641

Protein

Subunits of ribonucleoside-diphosphate reductase 2

could be indirect


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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 

MATTTAECLT QETMDYHALN AMLNLYDSAG RIQFDKDRQA VDAFIATHVR PNSVTFSSQQ
QRLNWLVNEG YYDESVLNRY SRDFVITLFT HAHTSGFRFQ TFLGAWKFYT SYTLKTFDGK
RYLEDFADRV TMVALTLAQG DETLALQLTD EMLSGRFQPA TPTFLNCGKQ QRGELVSCFL
LRIEDNMESI GRAVNSALQL SKRGGGVAFL LSNLREAGAP IKRIENQSSG VIPVMKMLED
AFSYANQLGA RQGAGAVYLH AHHPDILRFL DTKRENADEK IRIKTLSLGV VIPDITFHLA
KENAQMALFS PYDVERVYGK PFADVAISQH YDELVADERI RKKYLNARDF FQRLAEIQFE
SGYPYIMYED TVNRANPIAG RINMSNLCSE ILQVNSASEY DENLDYTRTG HDISCNLGSL
NIAHTMDSPD FARTVETAVR GLTAVSDMSH IRSVPSIEAG NAASHAIGLG QMNLHGYLAR
EGIAYGSPEA LDFTNLYFYA ITWHALRTSM LLARERGETF AGFKQSRYAS GEYFSQYLQG
NWQPKTAKVG ELFTRSGITL PTREMWAQLR DDVMRYGIYN QNLQAVPPTG SISYINHATS
SIHPIVAKVE IRKEGKTGRV YYPAPFMTNE NLALYQDAYE IGAEKIIDTY AEATRHVDQG
LSLTLFFPDT ATTRDINKAQ IYAWRKGIKT LYYIRLRQMA LEGTEIEGCV SCAL
Length

714

Mol. Wt

80.481 kDa

pI

6.5 (calculated)

Extinction coefficient

88,130 - 89,005 (calc based on 37 Y, 6 W, and 7 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 (By similarity)

UniProt:P39452

Domain

98..172

PF00317 Ribonucleotide reductase, all-alpha domain

PMID:19920124

Domain

175..694

PF02867 Ribonucleotide reductase, barrel domain

PMID:19920124

Domain

16..97

PF08343 Ribonucleotide reductase N-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=nrdE 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:16130589

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947155

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008806

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P39452

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG20257

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG20257

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947155

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002450

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4158

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

62

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

30

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

42

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)

nrdHIEF

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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_000913:2799350..2799390 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:b2675 (EcoliWiki Page)

NCBI GEO profiles for nrdE

microarray

GenExpDB:b2675 (EcoliWiki Page)

Summary of data for nrdE 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 nrdE Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG20257

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4158

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2675

EcoGene

EcoGene:EG20257

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002450

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008806

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

Xenopus tropicalis

  • ENSXETP00000002508 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

NRDE

From SHIGELLACYC

E. coli O157

NRDE

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

Superfamily (EcoliWiki Page)

SUPERFAMILY:48168

Superfamily (EcoliWiki Page)

SUPERFAMILY:51998

Panther (EcoliWiki Page)

PTHR11573:SF4

Pfam (EcoliWiki Page)

PF00317 Ribonucleotide reductase, all-alpha domain

Pfam (EcoliWiki Page)

PF02867 Ribonucleotide reductase, barrel domain

Pfam (EcoliWiki Page)

PF08343 Ribonucleotide reductase N-terminal

EcoCyc

EcoCyc:EG20257

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG20257

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002450

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4158

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008806

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. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 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 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 3.4 3.5 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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).

Categories

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