torZ: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

torZ

Gene Synonym(s)

ECK1873, b1872, JW1861, bisZ[1], bisZ

Product Desc.

trimethylamine N-oxide reductase III, TorZ subunit[2][3];

Component of trimethylamine N-oxide reductase III[2][3]

Periplasmic trimethylamine oxide (TMAO) reductase; also has biotin sulfoxide and DMSO reductase activities; respiratory system[4]

Product Synonyms(s)

trimethylamine N-oxide reductase system III, catalytic subunit[1], B1872[2][1], TorZ[2][1], BisZ[2][1] , bisZ, ECK1873, JW1861, b1872

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): torYZ[2], yecK-bisZ

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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Verified Tat substrate: TorZ has a Tat/Sec (Class II) predicted 37 aa signal peptide (Tullman-Ercek, 2007). Signal peptide is a TatC-dependent export substrate (Gon, 2000).[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

torZ

Mnemonic

Trimethylamine oxide reductase

Synonyms

ECK1873, b1872, JW1861, bisZ[1], bisZ

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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

42.08 minutes 

MG1655: 1955031..1952602
<gbrowseImage> name=NC_000913:1952602..1955031 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1935777..1933348
<gbrowseImage> name=NC_012967:1933348..1935777 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1844661..1847090
<gbrowseImage> name=NC_012759:1844661..1847090 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1958721..1956292
<gbrowseImage> name=NC_007779:1956292..1958721 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2045602..2043173
<gbrowseImage> name=NC_010473:2043173..2045602 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

1952605

Edman degradation

PMID:11004177


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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

ΔtorZ (Keio:JW1861)

deletion

deletion

PMID:16738554

Shigen
CGSC9551[5]

ΔtorZ726::kan

PMID:16738554

CGSC:103190


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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

JW1861

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACATTAACAAGACGTGAATT

Primer 2:CCgGCCTGAACAGCTGGCTGATC

20H4

Kohara Phage

Genobase

PMID:3038334

12C7

Kohara Phage

Genobase

PMID:3038334

eda-51::Tn10

Linked marker

CAG18486 = CGSC7392[5]

est. P1 cotransduction: 43% [6]

uvrC279::Tn10

Linked marker

CAG12156 = CGSC7394[5]

est. P1 cotransduction: 21% [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:G7022

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13276

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003609

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946389

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3061

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006244

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

TorZ

Synonyms

trimethylamine N-oxide reductase system III, catalytic subunit[1], B1872[2][1], TorZ[2][1], BisZ[2][1] , bisZ, ECK1873, JW1861, b1872

Product description

trimethylamine N-oxide reductase III, TorZ subunit[2][3];

Component of trimethylamine N-oxide reductase III[2][3]

Periplasmic trimethylamine oxide (TMAO) reductase; also has biotin sulfoxide and DMSO reductase activities; respiratory system[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:0030288

outer membrane-bounded periplasmic space

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0009054

electron acceptor activity

1

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0005488

binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR009010

F

Seeded from EcoCyc (v14.0)

complete

GO:0009055

electron carrier activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006655

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006655

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006656

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006657

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006658

F

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:0030151

molybdenum ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006657

F

Seeded from EcoCyc (v14.0)

complete

GO:0030151

molybdenum ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0500

F

Seeded from EcoCyc (v14.0)

complete

GO:0042597

periplasmic space

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0574

C

Seeded from EcoCyc (v14.0)

complete

GO:0042597

periplasmic space

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0200

C

Seeded from EcoCyc (v14.0)

complete

GO:0050626

trimethylamine-N-oxide reductase (cytochrome c) activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.7.2.3

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006658

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 trimethylamine N-oxide reductase III

could be indirect

Protein

groL

PMID:16606699

Experiment(s):EBI-1141136

Protein

acnB

PMID:16606699

Experiment(s):EBI-1141136

Protein

eno

PMID:19402753

LCMS(ID Probability):99.6

Protein

hns

PMID:19402753

LCMS(ID Probability):99.6

Protein

fimA

PMID:19402753

LCMS(ID Probability):99.5

Protein

rpsF

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsT

PMID:19402753

LCMS(ID Probability):99.5

Protein

rplK

PMID:19402753

LCMS(ID Probability):99.5

Protein

groS

PMID:19402753

LCMS(ID Probability):99.6

Protein

pgm

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmC

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753

LCMS(ID Probability):99.6

Protein

phoA

PMID:19402753

LCMS(ID Probability):99.4

Protein

rpsJ

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplI

PMID:19402753

LCMS(ID Probability):99.6

Protein

cspE

PMID:19402753

LCMS(ID Probability):99.4

Protein

yfbN

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

ompA

PMID:19402753

LCMS(ID Probability):99.6

Protein

yfcZ

PMID:19402753

LCMS(ID Probability):99.6

Protein

clpB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplW

PMID:19402753

LCMS(ID Probability):99.6

Protein

osmY

PMID:19402753

LCMS(ID Probability):99.6

Protein

cspC

PMID:19402753

LCMS(ID Probability):99.6

Protein

ydjA

PMID:19402753

LCMS(ID Probability):99.4

Protein

lpp

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplL

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

periplasm

Periplasm

PMID:11004177

EchoLocation:torZ


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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 

MIREEVMTLT RREFIKHSGI AAGALVVTSA APLPAWAEEK GGKILTAGRW GAMNVEVKDG
KIVSSTGALA KTIPNSLQST AADQVHTTAR IQHPMVRKSY LDNPLQPAKG RGEDTYVQVS
WEQALKLIHE QHDRIRKANG PSAIFAGSYG WRSSGVLHKA QTLLQRYMNL AGGYSGHSGD
YSTGAAQVIM PHVVGSVEVY EQQTSWPLIL ENSQVVVLWG MNPLNTLKIA WSSTDEQGLE
YFHQLKKSGK PVIAIDPIRS ETIEFFDDNA TWIAPNMGTD VALMLGIAHT LMTQGKHDKV
FLEKYTTGYP QFEEYLTGKS DNTPKSAVWA AEITGVPEAQ IVKLAELMAA NRTMLMAGWG
IQRQQYGEQK HWMLVTLAAM LGQIGTPGGG FGFSYHYSNG GNPTRVGGVL PEMSAAIAGH
ASEAADDGGM TAIPVARIVD ALENPGGKYQ HNGKEQTYPN IKMIWWAGGG NFTHHQDTNR
LIKAWQKPEM IVVSECYWTA AAKHADIVLP ITTSFERNDL TMTGDYSNQH IVPMKQAVAP
QFEARNDFDV FADLAELLKP GGKEIYTEGK DEMAWLKFFY DAAQKGARAQ RVTMPMFNAF
WQQNKLIEMR HSEKNEQYVR YGDFRADPVK NALGTPSGKI EIYSKTLEKF GYKDCPAHPT
WLAPDEWKGT ADEKQLQLLT AHPAHRLHSQ LNYAELRKKY AIADREPITI HTEDAARFGI
ANGDLVRVWN KRGQILTGAV VTDGIKKGVV CVHEGAWPDL ENGLCKNGSA NVLTADIPSS
QLANACAGNS ALVYIEKYTG NAPKLTAFDQ PAVQA
Length

815

Mol. Wt

89.722 kDa

pI

7.2 (calculated)

Extinction coefficient

157,220 - 157,845 (calc based on 28 Y, 21 W, and 5 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

motif

1-31

UniProt Manual:Signal Peptides

UniProt:P46923

Domain

84..551

PF00384 Molybdopterin oxidoreductase

PMID:19920124

Domain

670..785

PF01568 Molydopterin dinucleotide binding domain

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=torZ 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:90111350

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946389

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006244

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P46923

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7022

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13276

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946389

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003609

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3061

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

16

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

10

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

19a

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)

torYZ

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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_000913:1955011..1955051 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

</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

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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:b1872 (EcoliWiki Page)

NCBI GEO profiles for torZ

microarray

GenExpDB:b1872 (EcoliWiki Page)

Summary of data for torZ 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 torZ Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G7022

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3061

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1872

EcoGene

EcoGene:EG13276

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003609

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006244

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

  • ENSXETP00000012907 (score: 1.000; bootstrap: 87%)

From Inparanoid:20070104

Shigella flexneri

BISZ

From SHIGELLACYC

E. coli O157

BISZ

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)

PF01568 Molydopterin dinucleotide binding domain

Pfam (EcoliWiki Page)

PF00384 Molybdopterin oxidoreductase

Superfamily (EcoliWiki Page)

SUPERFAMILY:50692

Panther (EcoliWiki Page)

PTHR11615:SF19

Superfamily (EcoliWiki Page)

SUPERFAMILY:53706

EcoCyc

EcoCyc:G7022

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13276

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003609

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3061

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006244

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 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 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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