Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 69.02 kDa 
• Atom Count: 4,330 
• Modelled Residue Count: 490 
• Deposited Residue Count: 548 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 6IDE

Crystal structure of the Vibrio cholera VqmA-Ligand-DNA complex provides molecular mechanisms for drug design

• PDB DOI: 10.2210/pdb6IDE/pdb
• NDB: 6IDE

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


• Deposited: 2018-09-09 Released: 2019-01-16 
• Deposition Author(s): Wu, H., Li, M.J., Guo, H.J., Zhou, H., Li, B., Xu, Q., Xu, C.Y., Yu, F., He, J.H.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.229 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Literature

Crystal structure of theVibrio choleraeVqmA-ligand-DNA complex provides insight into ligand-binding mechanisms relevant for drug design.

Wu, H., Li, M., Guo, H., Zhou, H., Li, B., Xu, Q., Xu, C., Yu, F., He, J.

(2019) J Biol Chem 294: 2580-2592

• PubMed: 30610119 
• DOI: 10.1074/jbc.RA118.006082
• Primary Citation of Related Structures:  
  6IDE


• PubMed Abstract: 
  

VqmA is a highly conserved transcriptional regulator of the quorum-sensing system of Vibrio cholerae , a major human pathogen that continues to imperil human health. VqmA represses biofilm formation and plays an important role in V. cholerae pathogenicity in the human host. Although VqmA's biological function is well understood, the molecular mechanisms by which its specific ligand (and effector), 3,5-dimethylpyrazine-2-ol (DPO), controls transcription of the target gene, vqmR , remain obscure. To elucidate the molecular mechanism of DPO binding, we used structural analyses and biochemical assays to study the V. cholerae VqmA-DPO-DNA complex. These analyses revealed that VqmA contains an N-terminal homodimer domain (PAS) and a C-terminal DNA-binding domain (DBD). We observed that VqmA directly binds to a DPO molecule via a compact hydrophobic pocket, consisting of a six-stranded antiparallel β-sheet and several α-helices. We also found that the VqmA dimer interacts with the quasi-palindromic sequence of the vqmR promoter through its DBD. The results of the biochemical studies indicated that a water atom and VqmA residues Phe-67 and Lys-101 play a key role in effector recognition, which is also assisted by Tyr-36 and Phe-99. This is the first molecular level view of the VqmA dimer bound to DPO and DNA. The structure-function analyses presented here improve our understanding of the complex mechanisms in the transcriptional regulation of VqmA in Vibrio spp. and may inform the design of drugs to manage V. cholerae infections.

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Organizational Affiliation: 

From the Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 and [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator LuxR family	A, B	256	Vibrio cholerae	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*AP*AP*AP*TP*CP*CP*CP*CP*CP*CP*T)-3')	C	18	Vibrio cholerae

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*AP*TP*TP*TP*CP*CP*CP*CP*CP*CP*T)-3')	D	18	Vibrio cholerae

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1U	E [auth A], F [auth B]	3,5-dimethylpyrazin-2-ol C6 H8 N2 O AJYKJVCIKQEVCF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.229 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.78	α = 90
b = 108.98	β = 90
c = 214.32	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
CRANK2	phasing
PDB_EXTRACT	data extraction
xia2	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Wu, H., Li, M.J., Guo, H.J., Zhou, H., Li, B., Xu, Q., Xu, C.Y., Yu, F., He, J.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31570740
National Natural Science Foundation of China	China	81330076

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2019-03-06
  Changes: Data collection, Database references