5FHK

Regulatory domain of AphB in Vibrio vulnificus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of the Regulatory Domain of AphB from Vibrio vulnificus, a Virulence Gene Regulator

Park, N.Song, S.Choi, G.Jang, K.K.Jo, I.Choi, S.H.Ha, N.-C.

(2017) Mol Cells 40: 299-306

  • DOI: 10.14348/molcells.2017.0015
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The transcriptional activator AphB has been implicated in acid resistance and pathogenesis in the food borne pathogens Vibrio vulnificus and Vibrio cholerae . To date, the full-length AphB crystal structure of V. cholerae ha ...

    The transcriptional activator AphB has been implicated in acid resistance and pathogenesis in the food borne pathogens Vibrio vulnificus and Vibrio cholerae . To date, the full-length AphB crystal structure of V. cholerae has been determined and characterized by a tetrameric assembly of AphB consisting of a DNA binding domain and a regulatory domain (RD). Although acidic pH and low oxygen tension might be involved in the activation of AphB, it remains unknown which ligand or stimulus activates AphB at the molecular level. In this study, we determine the crystal structure of the AphB RD from V. vulnificus under aerobic conditions without modification at the conserved cysteine residue of the RD, even in the presence of the oxidizing agent cumene hydroperoxide. A cysteine to serine amino acid residue mutant RD protein further confirmed that the cysteine residue is not involved in sensing oxidative stress in vitro. Interestingly, an unidentified small molecule was observed in the inter-subdomain cavity in the RD when the crystal was incubated with cumene hydroperoxide molecules, suggesting a new ligand-binding site. In addition, we confirmed the role of AphB in acid tolerance by observing an aphB -dependent increase in cadC transcript level when V. vulnificus was exposed to acidic pH. Our study contributes to the understanding of the AphB molecular mechanism in the process of recognizing the host environment.


    Organizational Affiliation

    Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LysR family transcriptional regulator
A, B, C, D, E, F
207Vibrio vulnificusMutation(s): 0 
Gene Names: JS86_04620CRN32_11180CRN34_08615CRN46_12435CRN58_12665D8T65_02215
Find proteins for A0A087IWB4 (Vibrio vulnificus)
Go to UniProtKB:  A0A087IWB4
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.965α = 90
b = 187.926β = 90
c = 57.36γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing
HKL-2000data scaling
PHENIXdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2015-12-22 
  • Released Date: 2017-01-11 
  • Deposition Author(s): Song, S., Ha, N.-C.

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-05-10
    Changes: Database references
  • Version 1.2: 2017-05-24
    Changes: Database references