7JU3 | pdb_00007ju3

MtrR bound to the mtrCDE operator from Neisseria gonorrhoeae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.282 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7JU3

This is version 1.3 of the entry. See complete history

Literature

Structures of Neisseria gonorrhoeae MtrR-operator complexes reveal molecular mechanisms of DNA recognition and antibiotic resistance-conferring clinical mutations.

Beggs, G.A.Ayala, J.C.Kavanaugh, L.G.Read, T.D.Hooks, G.M.Schumacher, M.A.Shafer, W.M.Brennan, R.G.

(2021) Nucleic Acids Res 49: 4155-4170

  • DOI: https://doi.org/10.1093/nar/gkab213
  • Primary Citation Related Structures: 
    7JNP, 7JU3

  • PubMed Abstract: 

    Mutations within the mtrR gene are commonly found amongst multidrug resistant clinical isolates of Neisseria gonorrhoeae, which has been labelled a superbug by the Centers for Disease Control and Prevention. These mutations appear to contribute to antibiotic resistance by interfering with the ability of MtrR to bind to and repress expression of its target genes, which include the mtrCDE multidrug efflux transporter genes and the rpoH oxidative stress response sigma factor gene. However, the DNA-recognition mechanism of MtrR and the consensus sequence within these operators to which MtrR binds has remained unknown. In this work, we report the crystal structures of MtrR bound to the mtrCDE and rpoH operators, which reveal a conserved, but degenerate, DNA consensus binding site 5'-MCRTRCRN4YGYAYGK-3'. We complement our structural data with a comprehensive mutational analysis of key MtrR-DNA contacts to reveal their importance for MtrR-DNA binding both in vitro and in vivo. Furthermore, we model and generate common clinical mutations of MtrR to provide plausible biochemical explanations for the contribution of these mutations to multidrug resistance in N. gonorrhoeae. Collectively, our findings unveil key biological mechanisms underlying the global stress responses of N. gonorrhoeae.


  • Organizational Affiliation
    • Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA.

Macromolecule Content 

  • Total Structure Weight: 62.05 kDa 
  • Atom Count: 4,057 
  • Modeled Residue Count: 447 
  • Deposited Residue Count: 468 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HTH-type transcriptional regulator MtrR
A, B
213Neisseria gonorrhoeaeMutation(s): 0 
Gene Names: mtrR
UniProt
Find proteins for P39897 (Neisseria gonorrhoeae)
Explore P39897 
Go to UniProtKB:  P39897
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39897
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*AP*TP*CP*CP*GP*TP*GP*CP*AP*AP*TP*CP*GP*TP*GP*TP*AP*TP*GP*T)-3')21Neisseria gonorrhoeae
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*CP*AP*TP*AP*CP*AP*CP*GP*AP*TP*TP*GP*CP*AP*CP*GP*GP*AP*TP*A)-3')21Neisseria gonorrhoeae
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.282 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.273α = 90
b = 59.42β = 114.31
c = 69.508γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR05 AI048593-09
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1R01AI109096-01A1
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR37 AI021150-32
National Science Foundation (NSF, United States)United StatesDGE-1644868

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-04-21
    Changes: Database references
  • Version 1.2: 2021-04-28
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description