7V2B

Crystal Structure of VpsR display novel dimeric architecture and c-di-GMP binding: mechanistic implications in oligomerization, ATPase activity and DNA binding.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.219 

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Literature

Crystal Structure of VpsR Revealed Novel Dimeric Architecture and c-di-GMP Binding Site: Mechanistic Implications in Oligomerization, ATPase Activity and DNA Binding.

Chakrabortty, T.Roy Chowdhury, S.Ghosh, B.Sen, U.

(2022) J Mol Biol 434: 167354-167354

  • DOI: 10.1016/j.jmb.2021.167354
  • Primary Citation of Related Structures:  
    7V2B, 7V2V, 7V3W, 7V4E

  • PubMed Abstract: 
  • VpsR, the master regulator of biofilm formation in Vibrio cholerae, is an atypical NtrC1 type bEBP lacking residues essential for σ 54 -RNAP binding and REC domain phosphorylation. Moreover, transcription from P vpsL , a promoter of biofilm biosynthesis, has been documented in presence of σ 70 -RNAP/VpsR/c-di-GMP complex ...

    VpsR, the master regulator of biofilm formation in Vibrio cholerae, is an atypical NtrC1 type bEBP lacking residues essential for σ 54 -RNAP binding and REC domain phosphorylation. Moreover, transcription from P vpsL , a promoter of biofilm biosynthesis, has been documented in presence of σ 70 -RNAP/VpsR/c-di-GMP complex. It was proposed that c-di-GMP and VpsR together form an active transcription complex with σ 70 -RNAP. However, the impact of c-di-GMP imparted on VpsR that leads to transcription activation with σ 70 -RNAP remained elusive, largely due to the lack of the structure of VpsR and knowledge about c-di-GMP:VpsR interactions. In this direction we have solved the crystal structure of VpsR RA , containing REC and AAA + domains, in apo, AMPPNP/GMPPNP and c-di-GMP bound states. Structures of VpsR RA unveiled distinctive REC domain orientation that leads to a novel dimeric association and noncanonical ATP/GTP binding. Moreover, we have demonstrated that at physiological pH VpsR remains as monomer having no ATPase activity but c-di-GMP imparted cooperativity to convert it to dimer with potent activity. Crystal structure of c-di-GMP:VpsR RA complex reveals that c-di-GMP binds near the C-terminal end of AAA + domain. Trp quenching studies on VpsR R , VpsR A , VpsR RA , VpsR AD with c-di-GMP additionally demonstrated that c-di-GMP could potentially bind VpsR D . We propose that c-di-GMP mediated tethering of VpsR D with VpsR A could likely favor generating the specific protein-DNA architecture for transcription activation.


    Organizational Affiliation

    Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, HBNI, 1/AF Bidhan Nagar, Kolkata 700064, India. Electronic address: udayaditya.sen@saha.ac.in.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VpsRA,
B [auth D]
399Vibrio choleraeMutation(s): 0 
Gene Names: vpsR
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
C [auth A],
D
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.219 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.639α = 90
b = 118.639β = 90
c = 78.255γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Science & Technology (DST, India)IndiaEMR/2015/000780 Dated 18-07-2016

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release