yedZ:On One Page

From EcoliWiki
Jump to navigation Jump to search

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

Quickview

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Standard Name

yedZ

Gene Synonym(s)

ECK1968, b1972, JW1955[1], JW1955

Product Desc.

conserved inner membrane protein[2][3]

Inner membrane heme subunit for periplasmic YedYZ reductase[4]

Product Synonyms(s)

conserved inner membrane protein[1], YedZ[2][1], B1972[2][1] , ECK1968, JW1955, b1972

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yedY[2]

Regulation/Activity
Quick Links



        

edit table

See Help:Quickview for help with entering information in the Quickview table.

Notes

[back to top]


YedY is anchored to the membrane by the YedZ subunit. Topology mapped using protein fusions. EPR spectroscopy shows that YedZ has a HALS-type low-spin heme.[4]



Gene

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

[back to top]


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

Standard name

yedZ

Mnemonic

Systematic nomenclature

Synonyms

ECK1968, b1972, JW1955[1], JW1955

edit table


Notes

Location(s) and DNA Sequence

[back to top]


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

43.94 minutes 

MG1655: 2038507..2039142
<gbrowseImage> name=NC_000913:2038507..2039142 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1978482..1979117
<gbrowseImage> name=NC_012967:1978482..1979117 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1930990..1931625
<gbrowseImage> name=NC_012759:1930990..1931625 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2042620..2043255
<gbrowseImage> name=NC_007779:2042620..2043255 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2129515..2130150
<gbrowseImage> name=NC_010473:2129515..2130150 source=DH10B preset=GeneLocation </gbrowseImage>

edit table


Notes

Sequence Features

[back to top]


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

Feature Type Strain Genomic Location Evidence Reference Notes
edit table


Notes

Alleles and Phenotypes

[back to top]


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

ΔyedZ (Keio:JW1955)

deletion

deletion

PMID:16738554

Shigen

zed-3069::Tn10

Insertion at 2,038,764 bp in MG1655 (NC_000913)

adapted from Nichols et al.[5]

CAG18451 = CGSC7395[6]

Synonyms:

edit table


Notes

Genetic Interactions

[back to top]



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


Notes

Genetic Resources

[back to top]


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

Resource Resource Type Source Notes/Reference

JW1955

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCGTCTGACAGCAAAACAGGT

Primer 2:CCTACAGATAATTTGTTGTGAAC

9G6

Kohara Phage

Genobase

PMID:3038334

uvrC279::Tn10

Linked marker

CAG12156 = CGSC7394[6]

est. P1 cotransduction: 11% [5]

zef-3129::Tn10

Linked marker

CAG12099 = CGSC7397[6]

est. P1 cotransduction: 14% [5]
Synonyms:zee-3129::Tn10

edit table


Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:G7060

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14048

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003646

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946483

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3801

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006542

Escherichia coli str. K-12 substr. MG1655

edit table


Notes

Links

[back to top]



Product(s)

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

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

Standard name

YedZ

Synonyms

conserved inner membrane protein[1], YedZ[2][1], B1972[2][1] , ECK1968, JW1955, b1972

Product description

conserved inner membrane protein[2][3]

Inner membrane heme subunit for periplasmic YedYZ reductase[4]

EC number (for enzymes)


edit table


Notes

Function

[back to top]


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:0005887

integral to plasma membrane

PMID:11867724[7]

IDA: Inferred from Direct Assay

C

complete

GO:0005506

iron ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013130

F

Seeded from EcoCyc (v14.0)

complete

GO:0009055

electron carrier activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013130

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013130

F

Seeded from EcoCyc (v14.0)

complete

GO:0050660

FAD binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013130

F

Seeded from EcoCyc (v14.0)

complete

edit table

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
edit table


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

C-terminus localized in the cytoplasm with 6 predicted transmembrane domains

Daley et al. (2005) [8]

plasma membrane


edit table


Notes

Structure and Physical Properties

[back to top]


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 

MRLTAKQVTW LKVCLHLAGL LPFLWLVWAI NHGGLGADPV KDIQHFTGRT ALKFLLATLL
ITPLARYAKQ PLLIRTRRLL GLWCFAWATL HLTSYALLEL GVNNLALLGK ELITRPYLTL
GIISWVILLA LAFTSTQAMQ RKLGKHWQQL HNFVYLVAIL APIHYLWSVK IISPQPLIYA
GLAVLLLALR YKKLRSLFNR LRKQVHNKLS V
Length

211

Mol. Wt

24.069 kDa

pI

11.2 (calculated)

Extinction coefficient

54,430 - 54,680 (calc based on 7 Y, 8 W, and 2 C residues)

edit table


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

18..162

PF01794 Ferric reductase like transmembrane component

PMID:19920124[9]

edit table

<motif_map/>

tmhmm.php?gene=yedZ&show=pic&.jpg
Click the image to view raw output from TMHMM.

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

Structures

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

Models

View models at:

edit table

Structure figures

Notes

Gene Product Resources

[back to top]


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

Resource type Source Notes/Reference
edit table


Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16129918

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946483

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006542

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P76343

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7060

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14048

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946483

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003646

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3801

Escherichia coli str. K-12 substr. MG1655

edit table


Notes

Links

[back to top]




Expression

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]


See Help:Cellular levels

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

Protein

E. coli K-12 MG1655

15a

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

27

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

edit table

Notes

Transcription and Transcriptional Regulation

[back to top]


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

Transcription unit(s)

yedY

edit table
Figure courtesy of RegulonDB


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

[back to top]


<gbrowseImage> name=NC_000913:2038487..2038527 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.


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

</protect>

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

[back to top]


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

Allele Name Mutation Phenotype Reference
edit table


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

Type Reference Notes

microarray

GEO Profiles:b1972 (EcoliWiki Page)

NCBI GEO profiles for yedZ

microarray

GenExpDB:b1972 (EcoliWiki Page)

Summary of data for yedZ from multiple microarray studies

edit table


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

Resource Name Resource Type Description Source Notes
edit table

<protect>

Notes

Accessions Related to yedZ Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:G7060

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3801

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1972

EcoGene

EcoGene:EG14048

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003646

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006542

Escherichia coli str. K-12 substr. MG1655

edit table


Notes

Links

[back to top]



Evolution

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]


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

Organism Homologs (Statistics) Comments

Anopheles gambiae

  • ENSANGP00000000008 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

S2116

From SHIGELLACYC

E. coli O157

Z3064

From ECOO157CYC

edit table


Do-It-Yourself Web Tools


Notes

Families

[back to top]


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

Database Accession Notes

Pfam (EcoliWiki Page)

PF01794 Ferric reductase like transmembrane component

EcoCyc

EcoCyc:G7060

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14048

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003646

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3801

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006542

Escherichia coli str. K-12 substr. MG1655

edit table


Notes

Links

[back to top]



References

[back to top]


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 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 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 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).
  6. ↑ 6.0 6.1 6.2 CGSC: The Coli Genetics Stock Center
  7. ↑ Drew, D et al. (2002) Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis. Proc. Natl. Acad. Sci. U.S.A. 99 2690-5 PubMed
  8. ↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
  9. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=yedZ:On_One_Page&oldid=220367"