narY: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

narY

Gene Synonym(s)

ECK1461, b1467, JW1462, chlZ[1], chlZ

Product Desc.

nitrate reductase Z, β subunit[2][3];

Component of nitrate reductase Z[2][3]

Nitrate reductase II (NRZ), beta subunit[4]

Product Synonyms(s)

nitrate reductase 2 (NRZ), beta subunit[1], B1467[2][1], ChlZ[2][1], NarY[2][1] , chlZ, ECK1461, JW1462, b1467

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): narZYWV[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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Stationary phase induced, RpoS-dependent.[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

narY

Mnemonic

Nitrate reductase, nitrate regulation

Synonyms

ECK1461, b1467, JW1462, chlZ[1], chlZ

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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

33.09 minutes 

MG1655: 1536877..1535333
<gbrowseImage> name=NC_000913:1535333..1536877 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1513004..1511460
<gbrowseImage> name=NC_012967:1511460..1513004 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1427392..1428936
<gbrowseImage> name=NC_012759:1427392..1428936 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1540567..1539023
<gbrowseImage> name=NC_007779:1539023..1540567 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1627472..1625928
<gbrowseImage> name=NC_010473:1625928..1627472 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

1535333

Edman degradation

PMID:2233673


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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

ΔnarY (Keio:JW1462)

deletion

deletion

PMID:16738554

Shigen
CGSC9273[5]

ΔnarY760::kan

PMID:16738554

CGSC:102040


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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

JW1462

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAAATCCGTTCACAAGTCGG

Primer 2:CCTTCGCCCTCCGCTTTGTCGCG

6D4

Kohara Phage

Genobase

PMID:3038334

1G4

Kohara Phage

Genobase

PMID:3038334

trg-2::Tn10

Linked marker

CAG12026 = CGSC7376[5]

est. P1 cotransduction: 17% [6]

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[5]

est. P1 cotransduction: 99% [6]
Synonyms:zdc-235::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:EG10647

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10647

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000640

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946034

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0641

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004896

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

NarY

Synonyms

nitrate reductase 2 (NRZ), beta subunit[1], B1467[2][1], ChlZ[2][1], NarY[2][1] , chlZ, ECK1461, JW1462, b1467

Product description

nitrate reductase Z, β subunit[2][3];

Component of nitrate reductase Z[2][3]

Nitrate reductase II (NRZ), beta subunit[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:0005506

iron ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0408

F

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:0008940

nitrate reductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006547

F

Seeded from EcoCyc (v14.0)

complete

GO:0008940

nitrate reductase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.7.99.4

F

Seeded from EcoCyc (v14.0)

complete

GO:0009055

electron carrier activity

PMID:2139607

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0009061

anaerobic respiration

PMID:4869216

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0009325

nitrate reductase complex

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006547

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: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:0019898

extrinsic to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9903

C

Seeded from EcoCyc (v14.0)

complete

GO:0022900

electron transport chain

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0249

P

Seeded from EcoCyc (v14.0)

complete

GO:0042126

nitrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006547

P

Seeded from EcoCyc (v14.0)

complete

GO:0042128

nitrate assimilation

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0534

P

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:0051538

3 iron, 4 sulfur cluster binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0003

F

Seeded from EcoCyc (v14.0)

complete

GO:0051538

3 iron, 4 sulfur cluster binding

PMID:1321049

IPI: Inferred from Physical Interaction

F

Seeded from EcoCyc (v14.0)

Missing: with/from

GO:0051539

4 iron, 4 sulfur cluster binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0004

F

Seeded from EcoCyc (v14.0)

complete

GO:0051539

4 iron, 4 sulfur cluster binding

PMID:1321049

IPI: Inferred from Physical Interaction

F

Seeded from EcoCyc (v14.0)

Missing: with/from

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006547

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

GO:0006974

response to DNA damage stimulus

PMID:11967071

IEP: Inferred from Expression Pattern

P

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 nitrate reductase Z

could be indirect

Protein

narG

PMID:15690043

Experiment(s):EBI-880251, EBI-880367

Protein

pepN

PMID:15690043

Experiment(s):EBI-880251

Protein

lacZ

PMID:16606699

Experiment(s):EBI-1139921

Protein

lon

PMID:16606699

Experiment(s):EBI-1139921

Protein

narZ

PMID:16606699

Experiment(s):EBI-1139921

Protein

amiA

PMID:16606699

Experiment(s):EBI-1139921

Protein

prs

PMID:16606699

Experiment(s):EBI-1139921

Protein

narH

PMID:15690043

Experiment(s):EBI-885557

Protein

fadH

PMID:15690043

Experiment(s):EBI-885557

Protein

pepN

PMID:19402753

MALDI(Z-score):26.909207

Protein

fadH

PMID:19402753

LCMS(ID Probability):99.6

Protein

narG

PMID:19402753

LCMS(ID Probability):96.3 MALDI(Z-score):26.348376

Protein

narH

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

plasma membrane

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 

MKIRSQVGMV LNLDKCIGCH TCSVTCKNVW TGREGMEYAW FNNVETKPGI GYPKNWEDQE
EWQGGWVRDV NGKIRPRLGN KMGVITKIFA NPVVPQIDDY YEPFTFDYEH LHSAPEGKHI
PTARPRSLID GKRMDKVIWG PNWEELLGGE FEKRARDRNF EAMQKEMYGQ FENTFMMYLP
RLCEHCLNPS CVATCPSGAI YKREEDGIVL IDQDKCRGWR LCISGCPYKK IYFNWKSGKS
EKCIFCYPRI ESGQPTVCSE TCVGRIRYLG VLLYDADRIE EAASTEREVD LYERQCEVFL
DPHDPSVIEE ALKQGIPQNV IDAAQRSPVY KMAMDWKLAL PLHPEYRTLP MVWYVPPLSP
IQSYADAGGL PKSEGVLPAI ESLRIPVQYL ANMLSAGDTG PVLRALKRMM AMRHYMRSQT
VEGVTDTRAI DEVGLSVAQV EEMYRYLAIA NYEDRFVIPT SHREMAGDAF AERNGCGFTF
GDGCHGSDSK FNLFNSSRID AINITEVRDK AEGE
Length

514

Mol. Wt

58.557 kDa

pI

5.9 (calculated)

Extinction coefficient

94,770 - 97,020 (calc based on 23 Y, 11 W, and 18 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
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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=narY 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:16129426

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946034

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004896

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P19318

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10647

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10647

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946034

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000640

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0641

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

3a

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

26

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

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)

narZYWV

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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_000913:1536857..1536897 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:b1467 (EcoliWiki Page)

NCBI GEO profiles for narY

microarray

GenExpDB:b1467 (EcoliWiki Page)

Summary of data for narY 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 narY Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10647

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0641

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1467

EcoGene

EcoGene:EG10647

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000640

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004896

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

Organism Homologs (Statistics) Comments
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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:54862

EcoCyc

EcoCyc:EG10647

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10647

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000640

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0641

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004896

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. ↑ 2.00 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 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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