8UF3

Structure of cytochrome c4 from Neisseria gonorrhoeae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The structure of the diheme cytochrome c 4 from Neisseria gonorrhoeae reveals multiple contributors to tuning reduction potentials.

Zhong, F.Reik, M.E.Ragusa, M.J.Pletneva, E.V.

(2024) J Inorg Biochem 253: 112496-112496

  • DOI: https://doi.org/10.1016/j.jinorgbio.2024.112496
  • Primary Citation of Related Structures:  
    8UF3

  • PubMed Abstract: 

    Cytochrome c 4 (c 4 ) is a diheme protein implicated as an electron donor to cbb 3 oxidases in multiple pathogenic bacteria. Despite its prevalence, understanding of how specific structural features of c 4 optimize its function is lacking. The human pathogen Neisseria gonorrhoeae (Ng) thrives in low oxygen environments owing to the activity of its cbb 3 oxidase. Herein, we report characterization of Ng c 4 . Spectroelectrochemistry experiments of the wild-type (WT) protein have shown that the two Met/His-ligated hemes differ in potentials by ∼100 mV, and studies of the two His/His-ligated variants provided unambiguous assignment of heme A from the N-terminal domain of the protein as the high-potential heme. The crystal structure of the WT protein at 2.45 Å resolution has revealed that the two hemes differ in their solvent accessibility. In particular, interactions made by residues His57 and Ser59 in Loop1 near the axial ligand Met63 contribute to the tight enclosure of heme A, working together with the surface charge, to raise the reduction potential of the heme iron in this domain. The structure reveals a prominent positively-charged patch, which encompasses surfaces of both domains. In contrast to prior findings with c 4 from Pseudomonas stutzeri, the interdomain interface of Ng c 4 contributes minimally to the values of the heme iron potentials in the two domains. Analyses of the heme solvent accessibility, interface properties, and surface charges offer insights into the interplay of these structural elements in tuning redox properties of c 4 and other multiheme proteins.


  • Organizational Affiliation

    Department of Chemistry, Dartmouth College, Hanover, NH 03755, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome C4
A, B
191Neisseria gonorrhoeae F62Mutation(s): 0 
Gene Names: NGK_0144
UniProt
Find proteins for B4RQ30 (Neisseria gonorrhoeae (strain NCCP11945))
Explore B4RQ30 
Go to UniProtKB:  B4RQ30
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4RQ30
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.047α = 90
b = 168.047β = 90
c = 168.047γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM098502
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM128663

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Structure summary