Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.73 kDa 
• Atom Count: 4978 
• Modelled Residue Count: 578 
• Deposited Residue Count: 582 
• Unique protein chains: 1

3SZP

Full-length structure of the Vibrio cholerae virulence activator, AphB, a member of the LTTR protein family

• PDB DOI: 10.2210/pdb3SZP/pdb

• Classification: TRANSCRIPTION
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-07-19 Released: 2011-11-23 
• Deposition Author(s): Taylor, J.L., De Silva, R.S., Kovacikova, G., Lin, W., Taylor, R.K., Skorupski, K., Kull, F.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.234 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 

Literature

The crystal structure of AphB, a virulence gene activator from Vibrio cholerae, reveals residues that influence its response to oxygen and pH.

Taylor, J.L., De Silva, R.S., Kovacikova, G., Lin, W., Taylor, R.K., Skorupski, K., Kull, F.J.

(2012) Mol Microbiol 83: 457-470

• PubMed: 22053934 
• DOI: 10.1111/j.1365-2958.2011.07919.x
• Primary Citation of Related Structures:  
  3SZP, 3T1B


• PubMed Abstract: 
  

Expression of the two critical virulence factors of Vibrio cholerae, toxin-coregulated pilus and cholera toxin, is initiated at the tcpPH promoter by the regulators AphA and AphB. AphA is a winged helix DNA-binding protein that enhances the ability of AphB, a LysR-type transcriptional regulator, to activate tcpPH expression. We present here the 2.2 Å X-ray crystal structure of full-length AphB. As reported for other LysR-type proteins, AphB is a tetramer with two distinct subunit conformations. Unlike other family members, AphB must undergo a significant conformational change in order to bind to DNA. We have found five independent mutations in the putative ligand-binding pocket region that allow AphB to constitutively activate tcpPH expression at the non-permissive pH of 8.5 and in the presence of oxygen. These findings indicate that AphB is responsive to intracellular pH as well as to anaerobiosis and that residues in the ligand-binding pocket of the protein influence its ability to respond to both of these signals. We have solved the structure of one of the constitutive mutants, and observe conformational changes that would allow DNA binding. Taken together, these results describe a pathway of conformational changes allowing communication between the ligand and DNA binding regions of AphB.

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Organizational Affiliation: 

Department of Chemistry, Dartmouth College, Hanover, NH 03755, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, LysR family	A, B	291	Vibrio cholerae	Mutation(s): 0  Gene Names: VC_1049
UniProt
Find proteins for Q9KT56 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KT56  Go to UniProtKB:  Q9KT56

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.234 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.209	α = 90
b = 106.1	β = 90
c = 167.846	γ = 90

Software Package:

Software Name	Purpose
JBluIce-EPICS	data collection
PHENIX	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-07-19 
• Released Date: 2011-11-23 
Deposition Author(s): Taylor, J.L., De Silva, R.S., Kovacikova, G., Lin, W., Taylor, R.K., Skorupski, K., Kull, F.J.

Revision History  

• Version 1.0: 2011-11-23
  Type: Initial release
  
• Version 1.1: 2012-02-01
  Changes: Database references