nikE: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

nikE

Gene Synonym(s)

ECK3464, b3480, JW3445, hydD, hydC[1], hydC

Product Desc.

NikE[2][3];

Component of nickel ABC transporter[2][3]

Nickel transport ATP-binding protein[4]

Product Synonyms(s)

nickel transporter subunit[1], ATP-binding component of ABC superfamily[1], B3480[2][1], HydC[2][1], HydD[2][1], NikE[2][1] , ECK3464, hydC, hydD, JW3445, b3480

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): nikABCDER[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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Mutants display nickel-remediated formate hydrogen-lyase, hydrogenase, and hydrogenase-related fumarase defects. Overexpression causes abnormal biofilm architecture.[4]



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

nikE

Mnemonic

Nickel

Synonyms

ECK3464, b3480, JW3445, hydD, hydC[1], hydC

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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

77.93 minutes 

MG1655: 3615799..3616605
<gbrowseImage> name=NC_000913:3615799..3616605 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3548464..3549270
<gbrowseImage> name=NC_012967:3548464..3549270 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3504293..3505099
<gbrowseImage> name=NC_012759:3504293..3505099 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4022639..4021833
<gbrowseImage> name=NC_007779:4021833..4022639 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3713544..3714350
<gbrowseImage> name=NC_010473:3713544..3714350 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

ΔnikE (Keio:JW3445)

deletion

deletion

PMID:16738554

Shigen
CGSC10556[5]

ΔnikE734::kan

PMID:16738554

CGSC:102074


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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

JW3445

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACTTTACTTAACATCTCCGG

Primer 2:CCAACCTTTTCTGTGGTGCGACG

10D10

Kohara Phage

Genobase

PMID:3038334

5F2

Kohara Phage

Genobase

PMID:3038334

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[5]

est. P1 cotransduction: 40% [6]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[5]

est. P1 cotransduction: % [6]

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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:EG12079

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12079

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001985

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947987

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2004

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011362

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

NikE

Synonyms

nickel transporter subunit[1], ATP-binding component of ABC superfamily[1], B3480[2][1], HydC[2][1], HydD[2][1], NikE[2][1] , ECK3464, hydC, hydD, JW3445, b3480

Product description

NikE[2][3];

Component of nickel ABC transporter[2][3]

Nickel transport ATP-binding protein[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:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

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:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003439

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015858

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017871

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:0005886

plasma membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014137

C

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0997

C

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-1003

C

Seeded from EcoCyc (v14.0)

complete

GO:0006810

transport

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0813

P

Seeded from EcoCyc (v14.0)

complete

GO:0015413

nickel-transporting ATPase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01712

F

Seeded from EcoCyc (v14.0)

complete

GO:0015413

nickel-transporting ATPase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014137

F

Seeded from EcoCyc (v14.0)

complete

GO:0015413

nickel-transporting ATPase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015858

F

Seeded from EcoCyc (v14.0)

complete

GO:0015413

nickel-transporting ATPase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.6.3.24

F

Seeded from EcoCyc (v14.0)

complete

GO:0015675

nickel ion transport

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01712

P

Seeded from EcoCyc (v14.0)

complete

GO:0015675

nickel ion transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014137

P

Seeded from EcoCyc (v14.0)

complete

GO:0015675

nickel ion transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015858

P

Seeded from EcoCyc (v14.0)

complete

GO:0015675

nickel ion transport

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0921

P

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015858

C

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc (v14.0)

complete

GO:0016151

nickel ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014137

F

Seeded from EcoCyc (v14.0)

complete

GO:0016151

nickel ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0533

F

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc (v14.0)

complete

GO:0016887

ATPase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003439

F

Seeded from EcoCyc (v14.0)

complete

GO:0016887

ATPase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017871

F

Seeded from EcoCyc (v14.0)

complete

GO:0017111

nucleoside-triphosphatase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

PMID:11967071

IEP: Inferred from Expression Pattern

P

complete

GO:0019898

extrinsic to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9903

C

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 nickel ABC transporter

could be indirect

Protein

groL

PMID:16606699

Experiment(s):EBI-1146002

Protein

dnaK

PMID:16606699

Experiment(s):EBI-1146002

Protein

rplB

PMID:15690043

Experiment(s):EBI-879814

Protein

rpsC

PMID:15690043

Experiment(s):EBI-879814

Protein

rpsD

PMID:15690043

Experiment(s):EBI-879814

Protein

rpsG

PMID:15690043

Experiment(s):EBI-879814

Protein

secA

PMID:15690043

Experiment(s):EBI-879814

Protein

srmB

PMID:15690043

Experiment(s):EBI-879814

Protein

tufA

PMID:15690043

Experiment(s):EBI-879814

Protein

rpsD

PMID:19402753

MALDI(Z-score):35.547108

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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

cytoplasm

From EcoCyc[3]


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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 

MTLLNISGLS HHYAHGGFNG KHQHQAVLNN VSLTLKSGET VALLGRSGCG KSTLARLLVG
LESPAQGNIS WRGEPLAKLN RAQRKAFRRD IQMVFQDSIS AVNPRKTVRE ILREPMRHLL
SLKKSEQLAR ASEMLKAVDL DDSVLDKRPP QLSGGQLQRV CLARALAVEP KLLILDEAVS
NLDLVLQAGV IRLLKKLQQQ FGTACLFITH DLRLVERFCQ RVMVMDNGQI VETQVVGEKL
TFSSDAGRVL QNAVLPAFPV RRRTTEKV
Length

268

Mol. Wt

29.721 kDa

pI

10.5 (calculated)

Extinction coefficient

6,990 - 7,490 (calc based on 1 Y, 1 W, and 4 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

52..180

PF00005 ABC transporter

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=nikE 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:16131352

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947987

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011362

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P33594

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12079

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12079

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947987

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001985

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2004

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

Ecoli K-12

3.69+/-0.083

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.000620347

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

13a

molecules/cell/generation

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

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

Protein

E. coli K-12 MG1655

5a

molecules/cell/generation

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

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

Protein

E. coli K-12 MG1655

0a

molecules/cell/generation

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

Ribosome Profiling

Low confidence in the sequencing data set.

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)

nikABCDER

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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_000913:3615779..3615819 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:b3480 (EcoliWiki Page)

NCBI GEO profiles for nikE

microarray

GenExpDB:b3480 (EcoliWiki Page)

Summary of data for nikE 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 nikE Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG12079

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2004

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3480

EcoGene

EcoGene:EG12079

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001985

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011362

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

Drosophila melanogaster

  • FBgn0031362 (score: 1.000; bootstrap: 69%)
  • FBgn0032167 (score: 0.229)
  • FBgn0025683 (score: 0.225)
  • FBgn0020762 (score: 0.211)
  • FBgn0031516 (score: 0.208)
  • FBgn0031220 (score: 0.184)
  • FBgn0052091 (score: 0.175)
  • FBgn0031449 (score: 0.159)
  • FBgn0031515 (score: 0.153)
  • FBgn0003996 (score: 0.077)
  • FBgn0003515 (score: 0.074)
  • FBgn0020445 (score: 0.059)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA14594-PA (score: 1.000; bootstrap: 57%)
  • GA16356-PA (score: 0.236)
  • GA15545-PA (score: 0.235)
  • GA19180-PA (score: 0.225)
  • GA18458-PA (score: 0.185)
  • GA16671-PA (score: 0.176)
  • GA16397-PA (score: 0.154)
  • GA15454-PA (score: 0.057)

From Inparanoid:20070104

Shigella flexneri

NIKE

From SHIGELLACYC

E. coli O157

NIKE

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)

PF00005 ABC transporter

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

EcoCyc

EcoCyc:EG12079

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12079

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001985

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2004

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011362

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 3.4 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 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 5.2 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).

Categories

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