6NP6

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 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.267 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1107/S205979831900264X
  • Primary Citation of Related Structures:  
    6NP6, 5V30

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Crp/Fnr family transcriptional regulatorA, B154Porphyromonas 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.267 
  • 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

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

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