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dipZ:On One Page

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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]

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

Function from GO

Cellular Component

Biological Process

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

DNA display    Protein display    Pubmed(dipZ)    Textpresso(dipZ)

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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]

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

94 minutes, 94 minutes 

MG1655: 4363065..4361368
gbrowse_img.php?coord=4361368..4363065&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 4369720..4368023
gbrowse_img.php?coord=4368023..4369720&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 4463427..4461730
gbrowse_img.php?coord=4461730..4463427&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

REL606

NC_012967: 4343763..4342066
gbrowse_img.php?coord=4342066..4343763&genome=REL606&name=NC_012967&trackset=0&width=300&.png

BW2952

NC_012759: 4300103..4301800
gbrowse_img.php?coord=4300103..4301800&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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Notes

Sequence Features

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Feature typeLocationDescription
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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.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

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 Resources

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ResourceResource TypeSourceNotes/Reference

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

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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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG12178

EchoBASE (EcoliWiki Page)

EchoBASE:EB2095

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4136

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C5218

EcoGene (EcoliWiki Page)

EcoGene:EG12178

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:DSBD

CGSC (EcoliWiki Page)

CGSC:34213

ASAP (EcoliWikiPage)

ASAP:ABE-0013539


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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

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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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.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0047134

protein-disulfide reductase activity

GO_REF:0000003
GO_REF:0000020

IEA: Inferred from Electronic Annotation

EC:1.8.1.8
HAMAP:MF_00399

F

Seeded from EcoCyc 12.5 [5]

complete

GO:0045454

cell redox homeostasis

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006662

P

Seeded from EcoCyc 12.5 [5]

complete

GO:0017004

cytochrome complex assembly

GO_REF:0000002
GO_REF:0000004
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR003834
SP_KW:KW-0201
HAMAP:MF_00399

P

Seeded from EcoCyc 12.5 [5]

complete

GO:0016491

oxidoreductase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

F

Seeded from EcoCyc 12.5 [5]

complete

GO:0016021

integral to membrane

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0812

C

Seeded from EcoCyc 12.5 [5]

complete

GO:0016020

membrane

GO_REF:0000002
GO_REF:0000004
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR003834
SP_KW:KW-0397
SP_KW:KW-0472

C

Seeded from EcoCyc 12.5 [5]

complete

GO:0009055

electron carrier activity

GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00399

F

Seeded from EcoCyc 12.5 [5]

complete

GO:0006810

transport

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0813

P

Seeded from EcoCyc 12.5 [5]

complete

GO:0006790

sulfur metabolic process

P

Seeded from EcoCyc 11.1[6].

required fields missing

GO:0005887

integral to plasma membrane

PMID:19258316

IDA: Inferred from Direct Assay

C

complete

GO:0017004

cytochrome complex assembly

PMID:7957865

IMP: Inferred from Mutant Phenotype

P

complete

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Interactions

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Partner TypePartnerNotesReferencesEvidence
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Notes

Localization

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CompartmentDescriptionEvidenceSourceNotes

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[6]


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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

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.

TypeResiduesDescriptionNotesReferences

motif

1-19

UniProt Manual:Signal Peptides

UniProt:P36655


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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
  • Representative Escherichia coli structure:
    1JPE|A
    19-151 of 565 residues (E-value: 4e-71) (Percent Identity: 99.25)
  • Representative homolog:
    1VRS|A (Escherichia coli str. K-12 substr. W3110)
    1-143 of 565 residues (E-value: 7e-76) (Percent Identity: 99.30)
  • View the PDB Table for dipZ
Models

View models at:

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Structure figures

Notes

Gene Product Resources

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Resource typeSourceNotes/Reference
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Accessions in Other Databases

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:DSBD-MONOMER

UniProt (EcoliWiki Page)

UniProt:P36655

PFAM (EcoliWiki Page)

PFAM:PF02683

RefSeq (EcoliWiki Page)

RefSeq:NP_418559


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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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MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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Notes

Cellular Levels

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MoleculeOrganism or StrainMolecules per cellGrowth conditionsGrowth rateAssay usedNotesReference(s)
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Notes

Transcription and Transcriptional Regulation

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Transcription unit(s)

yjdC

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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

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gbrowse_img.php?coord=4363045..4363085&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&width=400&figure=Nterm&.png
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

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

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

TypeReferenceNotes

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 NameResource TypeDescriptionSourceNotes
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Notes

Accessions Related to dipZ Expression

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DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG12178

EchoBASE (EcoliWiki Page)

EchoBASE:EB2095

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4136

EcoGene (EcoliWiki Page)

EcoGene:EG12178


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Evolution

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Homologs in Other Organisms

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OrganismHomologs (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

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF02683


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Links

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References

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  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 EcoliWiki page
  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 EcoliWiki page
  5. ↑ 5.0 5.1 5.2 5.3 5.4 5.5 5.6 5.7 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  6. ↑ 6.0 6.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

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