7DWM | pdb_00007dwm

Crystal structure of the phage VqmA-DPO complex

• PDB DOI: https://doi.org/10.2210/pdb7DWM/pdb

• Classification: TRANSCRIPTION
• Organism(s): Hapunavirus VP882
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-01-17 Released: 2021-05-05 
• Deposition Author(s): Gu, Y., Yang, W.S.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.291 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.260 (Depositor) 

Starting Model: experimental

Literature

Understanding the mechanism of asymmetric gene regulation determined by the VqmA of vibriophage.

Gu, Y., Zhi, S.X., Yang, N., Yang, W.S.

(2021) Biochem Biophys Res Commun 558: 51-56

• PubMed: 33895551 
• DOI: https://doi.org/10.1016/j.bbrc.2021.04.036
• Primary Citation of Related Structures:  
  7DWM


• PubMed Abstract: 
  

  The quorum-sensing (QS) system between the phages and their hosts is important for the phage lysis-lysogeny decision. In Vibrio cholerae, the QS system consists of a LuxR-type receptor VqmA (VqmA _Vc ) and an autoinducer molecule 3,5-dimethylpyrazin-2-ol (DPO). A VqmA homolog encoded by vibriophage VP882 (VqmA _Phage ) can intervene the host QS system via binding to both the host-produced DPO and its cognate promoter (Pqtip) to induce the phage lysogeny-to-lysis transition, whereas VqmA _Vc cannot influence the VqmA _Phage -induced pathway, suggesting an asymmetry regulation. In this study, we report the crystal structure of VqmA _Phage -DPO complex at 2.65 Å and reveal that the mechanism of DPO recognition is conserved in VqmA homologs. Besides, we identify a non-classical palindrome sequence in Pqtip, which can be effectively recognized by VqmA _Phage but not VqmA _Vc . The sequence contains an interval longer than that in the vqmR promoter recognized by VqmA _Vc . In addition, the two DBD regions in the VqmA _Phage dimer exhibit more relaxed architecture than that of the reported VqmA _Vc , which is likely to be in the conformation that may easily bind to target promoter containing a longer interval. In summary, our findings provide a structural and biochemical basis for the DBD-dependent DNA recognition in different promoter regions in the phage lysogeny-to-lysis decision communication system, and provide clues for developing phage therapies against Vibrio cholerae infection.

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Organizational Affiliation: 
• State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, 300353, Tianjin, China.
State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, 300353, Tianjin, China. Electronic address: [e-mail].
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
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: 53.52 kDa 
• Atom Count: 3,507 
• Modeled Residue Count: 436 
• Deposited Residue Count: 476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator	A, B	238	Hapunavirus VP882	Mutation(s): 0
UniProt
Find proteins for A2I306 (Vibrio phage VP882) Explore A2I306  Go to UniProtKB:  A2I306

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1U (Subject of Investigation/LOI)	C [auth A], D [auth B]	3,5-dimethylpyrazin-2-ol C6 H8 N2 O AJYKJVCIKQEVCF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.291 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.260 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.664	α = 90
b = 133.664	β = 90
c = 89.514	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	refinement
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-05-05 
Deposition Author(s): Gu, Y., Yang, W.S.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31870737

Revision History  

• Version 1.0: 2021-05-05
  Type: Initial release
  
• Version 1.1: 2021-05-12
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description