6NP6 | pdb_00006np6

Crystal structure of the sensor domain of the transcriptional regulator HcpR from Porphyromonas Gingivalis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.294 (Depositor), 0.301 (DCC) 
  • R-Value Work: 
    0.264 (Depositor), 0.267 (DCC) 
  • R-Value Observed: 
    0.267 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Nitrosative Stress Sensing in Porphyromonas gingivalis: Structure and Mechanisms of the Heme Binding Transcriptional Regulator HcpR.

Belvin, B.R.Musayev, F.N.Turner, J.Scarsdale, J.N.Escalante, C.R.Lewis, J.P.

(2019) Acta Crystallogr D Struct Biol 75: 437-450

  • DOI: https://doi.org/10.1107/S205979831900264X
  • Primary Citation Related Structures: 
    5V30, 6NP6

  • PubMed Abstract: 

    Although the HcpR regulator plays a vital step in initiation of the nitrosative stress response in many Gram-negative anaerobic bacteria, the molecular mechanisms that it uses to mediate gas sensing are not well understood. Here, a 2.6 Å resolution crystal structure of the N-terminal sensing domain of the anaerobic periodontopathogen Porphyromonas gingivalis HcpR is presented. The protein has classical features of the regulators belonging to the FNR-CRP family and contains a hydrophobic pocket in its N-terminal sensing domain. It is shown that heme bound to HcpR exhibits heme iron as a hexacoordinate system in the absence of nitric oxide (NO) and that upon nitrosylation it transitions to a pentacoordinate system. Finally, small-angle X-ray scattering experiments on full-length HcpR reveal that the C-terminal DNA-binding domain of HcpR has a high degree of interdomain flexibility.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA.

Macromolecule Content 

  • Total Structure Weight: 34.49 kDa 
  • Atom Count: 2,371 
  • Modeled Residue Count: 304 
  • Deposited Residue Count: 308 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Crp/Fnr family transcriptional regulator
A, B
154Porphyromonas gingivalisMutation(s): 0 
Gene Names: CBG53_06810PGIN_13-1_00953
UniProt
Find proteins for Q7MVK4 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Explore Q7MVK4 
Go to UniProtKB:  Q7MVK4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7MVK4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.294 (Depositor), 0.301 (DCC) 
  • R-Value Work:  0.264 (Depositor), 0.267 (DCC) 
  • R-Value Observed: 0.267 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.468α = 90
b = 138.851β = 90
c = 44.546γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United States1R01DE023304
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United States1F31DE025158

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.2: 2022-03-23
    Changes: Author supporting evidence, Database references
  • Version 1.3: 2024-04-03
    Changes: Data collection, Refinement description