5D8C

Crystal structure of HiNmlR, a MerR family regulator lacking the sensor domain, bound to promoter DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis of thiol-based regulation of formaldehyde detoxification in H. influenzae by a MerR regulator with no sensor region.

Counago, R.M.Chen, N.H.Chang, C.W.Djoko, K.Y.McEwan, A.G.Kobe, B.

(2016) Nucleic Acids Res 44: 6981-6993

  • DOI: https://doi.org/10.1093/nar/gkw543
  • Primary Citation of Related Structures:  
    5D8C, 5D90, 5E01

  • PubMed Abstract: 

    Pathogenic bacteria such as Haemophilus influenzae, a major cause of lower respiratory tract diseases, must cope with a range of electrophiles generated in the host or by endogenous metabolism. Formaldehyde is one such compound that can irreversibly damage proteins and DNA through alkylation and cross-linking and interfere with redox homeostasis. Its detoxification operates under the control of HiNmlR, a protein from the MerR family that lacks a specific sensor region and does not bind metal ions. We demonstrate that HiNmlR is a thiol-dependent transcription factor that modulates H. influenzae response to formaldehyde, with two cysteine residues (Cys54 and Cys71) identified to be important for its response against a formaldehyde challenge. We obtained crystal structures of HiNmlR in both the DNA-free and two DNA-bound forms, which suggest that HiNmlR enhances target gene transcription by twisting of operator DNA sequences in a two-gene operon containing overlapping promoters. Our work provides the first structural insights into the mechanism of action of MerR regulators that lack sensor regions.


  • Organizational Affiliation

    School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Qld 4072, Australia Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Qld 4072, Australia Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia rafael.counago@sgc.ox.ac.uk.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MerR family regulator protein
A, B
137Haemophilus influenzae Rd KW20Mutation(s): 0 
Gene Names: HI_0186
UniProt
Find proteins for P44558 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore P44558 
Go to UniProtKB:  P44558
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP44558
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*TP*TP*AP*GP*AP*GP*TP*TP*CP*AP*CP*TP*CP*TP*AP*AP*G)-3')18Haemophilus influenzae Rd KW20
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*TP*TP*AP*GP*AP*GP*TP*GP*AP*AP*CP*TP*CP*TP*AP*AP*G)-3')18Haemophilus influenzae Rd KW20
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.03α = 90
b = 111.82β = 102.1
c = 103.17γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASESphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP0986578
National Health and Medical Research Council (NHMRC, Australia)Australia565526
National Health and Medical Research Council (NHMRC, Australia)Australia1071659

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-08-31
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description