dipZ: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

dsbD

Gene Synonym(s)

dipZ, ECK4130, b4136, JW5734, cutA2, cycZ, htrI, dsbD[1][2], htrI

Product Desc.

fused thiol:disulfide interchange protein[3]: membrane electron transporter[4]: activator of DsbC[1]

Product Synonyms(s)

B4136[2][1], HtrI[2][1], CycZ[2][1], DipZ, cutA2, cycZ, dipZ, ECK4130, htrI, JW5734, b4136

Function from GO

<GO_nr />

Knock-Out Phenotype

copper sensitivity PMID:8917542 PMID:16087673: temperature sensitivity PMID:7628442

Regulation/Expression
Regulation/Activity

The bacterial membrane protein DsbD transfers electrons across the cytoplasmic membrane to reduce protein disulfide bonds in extracytoplasmic proteins. Its substrates include protein disulfide isomerases and a protein involved in cytochrome c assembly. It has three domains, each containing two redox-active cysteines. Electrons are transferred between them through thiol-disulfide exchange reactions.

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

dsbD

Mnemonic

Disulfide bond

Synonyms

dipZ, ECK4130, b4136, JW5734, cutA2, cycZ, htrI, dsbD[1][2], htrI

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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

94 minutes, 94 minutes 

MG1655: 4363065..4361368
<gbrowseImage> name=NC_000913:4361368..4363065 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4369720..4368023
<gbrowseImage> name=NC_007779:4368023..4369720 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4463427..4461730
<gbrowseImage> name=NC_010473:4461730..4463427 source=DH10B preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4343763..4342066
<gbrowseImage> name=NC_012967:4342066..4343763 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4300103..4301800
<gbrowseImage> name=NC_012759:4300103..4301800 source=BW2952 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

ΔdipZ762::kan

PMID:16738554

CGSC:100610

dipZ4::Cm

PMID:8917542 PMID:9352906

CGSC:65873

ΔdsbD

PMID:9335267, PMID:10545108

This strain contains an internal in-frame deletion of 536 codons of the dsbD gene. We replaced the deleted DNA sequences by an EcoRI site,

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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

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

21H11

Kohara Phage

Genobase

PMID:3038334

5G7

Kohara Phage

Genobase

PMID:3038334

9B1

Kohara Phage

Genobase

PMID:3038334

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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:EG12178

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12178

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002071

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948649

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2095

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013539

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

DsbD

Synonyms

B4136[2][1], HtrI[2][1], CycZ[2][1], DipZ, cutA2, cycZ, dipZ, ECK4130, htrI, JW5734, b4136

Product description

fused thiol:disulfide interchange protein[3]: membrane electron transporter[4]: activator of DsbC[1]

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. 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:0016491

oxidoreductase activity

PMID:7628442

IDA: Inferred from Direct Assay

F

complete

GO:0005886

plasma membrane

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00399

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:0005887

integral to plasma membrane

PMID:19258316

IDA: Inferred from Direct Assay

C

complete

GO:0009055

electron carrier activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00399

F

Seeded from EcoCyc (v14.0)

complete

GO:0017004

cytochrome complex assembly

PMID:7957865

IMP: Inferred from Mutant Phenotype

P

complete

GO:0016020

membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003834

C

Seeded from EcoCyc (v14.0)

complete

GO:0006950

response to stress

PMID:7628442

IMP: Inferred from Mutant Phenotype

P

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:0042493

response to drug

PMID:7628442

IMP: Inferred from Mutant Phenotype

P

complete

GO:0016021

integral to membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0812

C

Seeded from EcoCyc (v14.0)

complete

GO:0071502

cellular response to temperature stimulus

PMID:7628442

IMP: Inferred from Mutant Phenotype

P

complete

GO:0016021

integral to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9909

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

PMID:7628442

C

Seeded from EcoCyc (v14.0)

Missing: evidence

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:0017004

cytochrome complex assembly

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00399

P

Seeded from EcoCyc (v14.0)

complete

GO:0017004

cytochrome complex assembly

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003834

P

Seeded from EcoCyc (v14.0)

complete

GO:0017004

cytochrome complex assembly

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0201

P

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:0045454

cell redox homeostasis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013766

P

Seeded from EcoCyc (v14.0)

complete

GO:0045454

cell redox homeostasis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017936

P

Seeded from EcoCyc (v14.0)

complete

GO:0045454

cell redox homeostasis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017937

P

Seeded from EcoCyc (v14.0)

complete

GO:0047134

protein-disulfide reductase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00399

F

Seeded from EcoCyc (v14.0)

complete

GO:0047134

protein-disulfide reductase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.8.1.8

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00399

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003834

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:0055114

oxidation reduction

PMID:7628442

IDA: Inferred from Direct Assay

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
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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

Inner membrane

N- and C-terminal two soluble domains localized to the periplasm with central 8 transmembrane segment domains

PMID:10712691 PMID:10545108

plasma membrane

From EcoCyc[5]


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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 

MAQRIFTLIL LLCSTSVFAG LFDAPGRSQF VPADQAFAFD FQQNQHDLNL TWQIKDGYYL
YRKQIRITPE HAKIADVQLP QGVWHEDEFY GKSEIYRDRL TLPVTINQAS AGATLTVTYQ
GCADAGFCYP PETKTVPLSE VVANNAAPQP VSVPQQEQPT AQLPFSALWA LLIGIGIAFT
PCVLPMYPLI SGIVLGGKQR LSTARALLLT FIYVQGMALT YTALGLVVAA AGLQFQAALQ
HPYVLIGLAI VFTLLAMSMF GLFTLQLPSS LQTRLTLMSN RQQGGSPGGV FVMGAIAGLI
CSPCTTAPLS AILLYIAQSG NMWLGGGTLY LYALGMGLPL MLITVFGNRL LPKSGPWMEQ
VKTAFGFVIL ALPVFLLERV IGDVWGLRLW SALGVAFFGW AFITSLQAKR GWMRIVQIIL
LAAALVSVRP LQDWAFGATH TAQTQTHLNF TQIKTVDELN QALVEAKGKP VMLDLYADWC
VACKEFEKYT FSDPQVQKAL ADTVLLQANV TANDAQDVAL LKHLNVLGLP TILFFDGQGQ
EHPQARVTGF MDAETFSAHL RDRQP
Length

565

Mol. Wt

61.796 kDa

pI

7.1 (calculated)

Extinction coefficient

84,340 - 85,340 (calc based on 16 Y, 11 W, and 8 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

1-19

UniProt Manual:Signal Peptides

UniProt:P36655

Domain

170..378

PF02683 Cytochrome C biogenesis protein transmembrane region

PMID:19920124

Domain

451..563

PF00085 Thioredoxin

PMID:19920124

Domain

22..140

PF11412 Disulphide bond corrector protein DsbC

PMID:19920124

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

<motif_map/>

tmhmm.php?gene=dsbD&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=dipZ 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:16131961

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948649

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013539

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P36655

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12178

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12178

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948649

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002071

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2095

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

456

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

145

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

221

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

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

456

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

145

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

221

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)

yjdC

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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_000913:4363045..4363085 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:b4136 (EcoliWiki Page)

NCBI GEO profiles for dsbD

microarray

GenExpDB:b4136 (EcoliWiki Page)

Summary of data for dsbD 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 dipZ Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG12178

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2095

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4136

EcoGene

EcoGene:EG12178

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002071

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013539

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

Arabidopsis thaliana

  • AT5G54290 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

DSBD

From SHIGELLACYC, found in beta and gamma proteobacteria

E. coli O157

DSBD

From ECOO157CYC

Caulobacter crescentus, Salmonella typhimurium

ScsB

PMID:15380548 PMID:9260936

eubacteria, archaea, plant (studied well in Rhodobacter capsulatus)

CcdA

PMID:12145197: homologs of transmembrane domain of DsbD: most of them contain only 6 transmembrane segments

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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)

PF02683 Cytochrome C biogenesis protein transmembrane region

Superfamily (EcoliWiki Page)

SUPERFAMILY:52833

Panther (EcoliWiki Page)

PTHR10438:SF20

Superfamily (EcoliWiki Page)

SUPERFAMILY:74863

Pfam (EcoliWiki Page)

PF00085 Thioredoxin

Pfam (EcoliWiki Page)

PF11412 Disulphide bond corrector protein DsbC

EcoCyc

EcoCyc:EG12178

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12178

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002071

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2095

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013539

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 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 2.7 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 Missiakas, D et al. (1995) Identification and characterization of a new disulfide isomerase-like protein (DsbD) in Escherichia coli. EMBO J. 14 3415-24 PubMed
  4. ↑ 4.0 4.1 Rietsch, A et al. (1996) An in vivo pathway for disulfide bond isomerization in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 93 13048-53 PubMed
  5. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

Categories

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