5G1K | pdb_00005g1k

A triple mutant of DsbG engineered for denitrosylation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.241 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5G1K

This is version 1.4 of the entry. See complete history

Literature

Sulfur Denitrosylation by an Engineered Trx-Like Dsbg Enzyme Identifies Nucleophilic Cysteine Hydrogen Bonds as Key Functional Determinant.

Lafaye, C.Van Molle, I.Tamu Dufe, V.Wahni, K.Boudier, A.Leroy, P.Collet, J.Messens, J.

(2016) J Biological Chem 291: 15020

  • DOI: https://doi.org/10.1074/jbc.M116.729426
  • Primary Citation Related Structures: 
    5G1K, 5G1L

  • PubMed Abstract: 

    Exposure of bacteria to NO results in the nitrosylation of cysteine thiols in proteins and low molecular weight thiols such as GSH. The cells possess enzymatic systems that catalyze the denitrosylation of these modified sulfurs. An important player in these systems is thioredoxin (Trx), a ubiquitous, cytoplasmic oxidoreductase that can denitrosylate proteins in vivo and S-nitrosoglutathione (GSNO) in vitro However, a periplasmic or extracellular denitrosylase has not been identified, raising the question of how extracytoplasmic proteins are repaired after nitrosative damage. In this study, we tested whether DsbG and DsbC, two Trx family proteins that function in reducing pathways in the Escherichia coli periplasm, also possess denitrosylating activity. Both DsbG and DsbC are poorly reactive toward GSNO. Moreover, DsbG is unable to denitrosylate its specific substrate protein, YbiS. Remarkably, by borrowing the CGPC active site of E. coli Trx-1 in combination with a T200M point mutation, we transformed DsbG into an enzyme highly reactive toward GSNO and YbiS. The pKa of the nucleophilic cysteine, as well as the redox and thermodynamic properties of the engineered DsbG are dramatically changed and become similar to those of E. coli Trx-1. X-ray structural insights suggest that this results from a loss of two direct hydrogen bonds to the nucleophilic cysteine sulfur in the DsbG mutant. Our results highlight the plasticity of the Trx structural fold and reveal that the subtle change of the number of hydrogen bonds in the active site of Trx-like proteins is the key factor that thermodynamically controls reactivity toward nitrosylated compounds.


  • Organizational Affiliation
    • From the de Duve Institute, Université Catholique de Louvain, B-1200 Brussels, Belgium, WELBIO, B-1200 Brussels, Belgium, the Brussels Center for Redox Biology, B-1050 Brussels, Belgium.

Macromolecule Content 

  • Total Structure Weight: 57.36 kDa 
  • Atom Count: 3,877 
  • Modeled Residue Count: 457 
  • Deposited Residue Count: 512 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
THIOL DISULFIDE INTERCHANGE PROTEIN DSBG
A, B
256Escherichia coliMutation(s): 3 
UniProt
Find proteins for P77202 (Escherichia coli (strain K12))
Explore P77202 
Go to UniProtKB:  P77202
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP77202
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.241 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.92α = 90
b = 57.22β = 94.75
c = 86.04γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-08
    Changes: Database references, Derived calculations
  • Version 1.2: 2016-07-27
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary