1VRS

Crystal structure of the disulfide-linked complex between the N-terminal and C-terminal domain of the electron transfer catalyst DsbD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis and kinetics of inter- and intramolecular disulfide exchange in the redox catalyst DsbD

Rozhkova, A.Stirnimann, C.U.Frei, P.Grauschopf, U.Brunisholz, R.Gruetter, M.G.Capitani, G.Glockshuber, R.

(2004) EMBO J 23: 1709-1719

  • DOI: 10.1038/sj.emboj.7600178
  • Primary Citation of Related Structures:  
    1VRS

  • PubMed Abstract: 
  • DsbD from Escherichia coli catalyzes the transport of electrons from cytoplasmic thioredoxin to the periplasmic disulfide isomerase DsbC. DsbD contains two periplasmically oriented domains at the N- and C-terminus (nDsbD and cDsbD) that are connected by a central transmembrane (TM) domain ...

    DsbD from Escherichia coli catalyzes the transport of electrons from cytoplasmic thioredoxin to the periplasmic disulfide isomerase DsbC. DsbD contains two periplasmically oriented domains at the N- and C-terminus (nDsbD and cDsbD) that are connected by a central transmembrane (TM) domain. Each domain contains a pair of cysteines that are essential for catalysis. Here, we show that Cys109 and Cys461 form a transient interdomain disulfide bond between nDsbD and cDsbD in the reaction cycle of DsbD. We solved the crystal structure of this catalytic intermediate at 2.85 A resolution, which revealed large relative domain movements in DsbD as a consequence of a strong overlap between the surface areas of nDsbD that interact with DsbC and cDsbD. In addition, we have measured the kinetics of all functional and nonfunctional disulfide exchange reactions between redox-active, periplasmic proteins and protein domains from the oxidative DsbA/B and the reductive DsbC/D pathway. We show that both pathways are separated by large kinetic barriers for nonfunctional disulfide exchange between components from different pathways.


    Organizational Affiliation

    Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Hönggerberg, Zürich, Switzerland.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thiol:disulfide interchange protein dsbDA,
C [auth B],
E [auth C]
143Escherichia coli str. K-12 substr. W3110Mutation(s): 1 
Gene Names: dsbDdipZcycZcutA2b4136
EC: 1.8.1.8
UniProt
Find proteins for P36655 (Escherichia coli (strain K12))
Explore P36655 
Go to UniProtKB:  P36655
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36655
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Thiol:disulfide interchange protein dsbDB [auth D],
D [auth E],
F
134Escherichia coli str. K-12 substr. W3110Mutation(s): 1 
Gene Names: dsbDdipZcycZcutA2b4136
EC: 1.8.1.8
UniProt
Find proteins for P36655 (Escherichia coli (strain K12))
Explore P36655 
Go to UniProtKB:  P36655
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36655
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.224 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 188.46α = 90
b = 52.6β = 100.39
c = 107.92γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references