4IP1 | pdb_00004ip1

C-terminal domain of the thiol:disulfide interchange protein DsbD, Q488K mutant

• PDB DOI: https://doi.org/10.2210/pdb4IP1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-01-09 Released: 2013-12-25 
• Deposition Author(s): Saridakis, E., Mavridou, D.A.I., Redfield, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 
  0.255 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

An Extended Active-site Motif Controls the Reactivity of the Thioredoxin Fold.

Mavridou, D.A., Saridakis, E., Kritsiligkou, P., Mozley, E.C., Ferguson, S.J., Redfield, C.

(2014) J Biological Chem 289: 8681-8696

• PubMed: 24469455 
• DOI: https://doi.org/10.1074/jbc.M113.513457
• Primary Citation Related Structures: 
  4IP1, 4IP6


• PubMed Abstract: 
  

  Proteins belonging to the thioredoxin (Trx) superfamily are abundant in all organisms. They share the same structural features, arranged in a seemingly simple fold, but they perform a multitude of functions in oxidative protein folding and electron transfer pathways. We use the C-terminal domain of the unique transmembrane reductant conductor DsbD as a model for an in-depth analysis of the factors controlling the reactivity of the Trx fold. We employ NMR spectroscopy, x-ray crystallography, mutagenesis, in vivo functional experiments applied to DsbD, and a comparative sequence analysis of Trx-fold proteins to determine the effect of residues in the vicinity of the active site on the ionization of the key nucleophilic cysteine of the -CXXC- motif. We show that the function and reactivity of Trx-fold proteins depend critically on the electrostatic features imposed by an extended active-site motif.

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Organizational Affiliation: 
• From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom and.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.63 kDa 
• Atom Count: 1,062 
• Modeled Residue Count: 121 
• Deposited Residue Count: 132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol:disulfide interchange protein DsbD	A	132	Escherichia coli K-12	Mutation(s): 1  Gene Names: dsbD, cutA2, cycZ, dipZ, b4136, JW5734 EC: 1.8.1.8
UniProt
Find proteins for P36655 (Escherichia coli (strain K12)) Explore P36655  Go to UniProtKB:  P36655

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free:  0.255 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.107	α = 90
b = 51.53	β = 90
c = 85.039	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-25 
Deposition Author(s): Saridakis, E., Mavridou, D.A.I., Redfield, C.

Revision History  

• Version 1.0: 2013-12-25
  Type: Initial release
  
• Version 1.1: 2014-02-12
  Changes: Database references
• Version 1.2: 2014-04-09
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Advisory, Refinement description
• Version 1.4: 2023-09-20
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary