5Y9S

Crystal structure of VV2_1132, a LysR family transcriptional regulator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A Novel Tetrameric Assembly Configuration in VV2_1132, a LysR-Type Transcriptional Regulator inVibrio vulnificus

Jang, Y.Choi, G.Hong, S.Jo, I.Ahn, J.Choi, S.H.Ha, N.C.

(2018) Mol Cells 41: 301-310

  • DOI: 10.14348/molcells.2018.2190
  • Primary Citation of Related Structures:  
    5Y9S

  • PubMed Abstract: 
  • LysR-type transcriptional regulators (LTTRs) contain an N-terminal DNA binding domain (DBD) and a C-terminal regulatory domain (RD). Typically, LTTRs function as homotetramers. VV2_1132 was identified in Vibrio vulnificus as an LTTR that is a homologue of HypT (also known as YjiE or QseD) in Escherichia coli ...

    LysR-type transcriptional regulators (LTTRs) contain an N-terminal DNA binding domain (DBD) and a C-terminal regulatory domain (RD). Typically, LTTRs function as homotetramers. VV2_1132 was identified in Vibrio vulnificus as an LTTR that is a homologue of HypT (also known as YjiE or QseD) in Escherichia coli . In this study, we determined the crystal structure of full-length VV2_1132 at a resolution of 2.2 Å, thereby revealing a novel combination of the domains in the tetrameric assembly. Only one DBD dimer in the tetramer can bind to DNA, because the DNA binding motifs of the other DBD dimer are completely buried in the tetrameric assembly. Structural and functional analyses of VV2_1132 suggest that it might not perform the same role as E. coli HypT, indicating that further study is required to elucidate the function of this gene in V. vulnificus . The unique structure of VV2_1132 extends our knowledge of LTTR function and mechanisms of action.


    Organizational Affiliation

    Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Seoul National University, Seoul 08826, Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VV2_1132A, B, C, D304Vibrio vulnificus CMCP6Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.669α = 90
b = 221.895β = 90
c = 57.875γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata collection
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry for Agriculture, Food and Rural AffairsKorea, Republic OfNRF-2017R1A2B2003992

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-05-09
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-23
    Changes: Data collection
  • Version 1.3: 2019-11-27
    Changes: Data collection