6G4R

Corynebacterium glutamicum OxyR C206S mutant, H2O2-bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural snapshots of OxyR reveal the peroxidatic mechanism of H2O2sensing.

Pedre, B.Young, D.Charlier, D.Mourenza, A.Rosado, L.A.Marcos-Pascual, L.Wahni, K.Martens, E.G de la Rubia, A.Belousov, V.V.Mateos, L.M.Messens, J.

(2018) Proc Natl Acad Sci U S A 115: E11623-E11632

  • DOI: https://doi.org/10.1073/pnas.1807954115
  • Primary Citation of Related Structures:  
    6G1B, 6G1D, 6G4R

  • PubMed Abstract: 
  • Hydrogen peroxide (H 2 O 2 ) is a strong oxidant capable of oxidizing cysteinyl thiolates, yet only a few cysteine-containing proteins have exceptional reactivity toward H 2 O 2 One such example is the prokaryotic transcription factor OxyR, which controls the antioxidant response in bacteria, and which specifically and rapidly reduces H 2 O 2 In this study, we present crystallographic evidence for the H 2 O 2 -sensing mechanism and H 2 O 2 -dependent structural transition of Corynebacterium glutamicum OxyR by capturing the reduced and H 2 O 2 -bound structures of a serine mutant of the peroxidatic cysteine, and the full-length crystal structure of disulfide-bonded oxidized OxyR ...

    Hydrogen peroxide (H 2 O 2 ) is a strong oxidant capable of oxidizing cysteinyl thiolates, yet only a few cysteine-containing proteins have exceptional reactivity toward H 2 O 2 One such example is the prokaryotic transcription factor OxyR, which controls the antioxidant response in bacteria, and which specifically and rapidly reduces H 2 O 2 In this study, we present crystallographic evidence for the H 2 O 2 -sensing mechanism and H 2 O 2 -dependent structural transition of Corynebacterium glutamicum OxyR by capturing the reduced and H 2 O 2 -bound structures of a serine mutant of the peroxidatic cysteine, and the full-length crystal structure of disulfide-bonded oxidized OxyR. In the H 2 O 2 -bound structure, we pinpoint the key residues for the peroxidatic reduction of H 2 O 2 , and relate this to mutational assays showing that the conserved active-site residues T107 and R278 are critical for effective H 2 O 2 reduction. Furthermore, we propose an allosteric mode of structural change, whereby a localized conformational change arising from H 2 O 2 -induced intramolecular disulfide formation drives a structural shift at the dimerization interface of OxyR, leading to overall changes in quaternary structure and an altered DNA-binding topology and affinity at the catalase promoter region. This study provides molecular insights into the overall OxyR transcription mechanism regulated by H 2 O 2 .


    Organizational Affiliation

    Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hydrogen peroxide-inducible genes activatorA [auth B]327Corynebacterium glutamicumMutation(s): 1 
Gene Names: C0I99_13405
UniProt
Find proteins for Q8NP91 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
Explore Q8NP91 
Go to UniProtKB:  Q8NP91
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NP91
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hydrogen peroxide-inducible genes activatorB [auth A],
D [auth G]
327Corynebacterium glutamicumMutation(s): 1 
Gene Names: C0I99_13405
UniProt
Find proteins for Q8NP91 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
Explore Q8NP91 
Go to UniProtKB:  Q8NP91
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NP91
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Hydrogen peroxide-inducible genes activatorC [auth E]327Corynebacterium glutamicumMutation(s): 1 
Gene Names: C0I99_13405
UniProt
Find proteins for Q8NP91 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
Explore Q8NP91 
Go to UniProtKB:  Q8NP91
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NP91
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEO
Query on PEO

Download Ideal Coordinates CCD File 
E [auth B],
H [auth E],
I [auth E]
HYDROGEN PEROXIDE
H2 O2
MHAJPDPJQMAIIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A [auth B]L-PEPTIDE LINKINGC3 H7 N O3 SCYS
OCS
Query on OCS
A [auth B]L-PEPTIDE LINKINGC3 H7 N O5 SCYS
CSD
Query on CSD
B [auth A],
D [auth G]
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.216α = 90
b = 56.991β = 98.02
c = 154.182γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateBelgiumHERC16
Other governmentBelgiumG.0D79.14N
Other privateBelgiumSRP34
Other privateSpainLE326U14
Other privateSpainUXXI2016/00127

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references