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Crystal Structure of VpsR Revealed Novel Dimeric Architecture and c-di-GMP Binding Site: Mechanistic Implications in Oligomerization, ATPase Activity and DNA Binding.
- Source :
-
Journal of molecular biology [J Mol Biol] 2022 Jan 30; Vol. 434 (2), pp. 167354. Date of Electronic Publication: 2021 Nov 10. - Publication Year :
- 2022
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Abstract
- VpsR, the master regulator of biofilm formation in Vibrio cholerae, is an atypical NtrC1 type bEBP lacking residues essential for σ <superscript>54</superscript> -RNAP binding and REC domain phosphorylation. Moreover, transcription from P <subscript>vpsL</subscript> , a promoter of biofilm biosynthesis, has been documented in presence of σ <superscript>70</superscript> -RNAP/VpsR/c-di-GMP complex. It was proposed that c-di-GMP and VpsR together form an active transcription complex with σ <superscript>70</superscript> -RNAP. However, the impact of c-di-GMP imparted on VpsR that leads to transcription activation with σ <superscript>70</superscript> -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 <superscript>RA</superscript> , containing REC and AAA <superscript>+</superscript> domains, in apo, AMPPNP/GMPPNP and c-di-GMP bound states. Structures of VpsR <superscript>RA</superscript> 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 <superscript>RA</superscript> complex reveals that c-di-GMP binds near the C-terminal end of AAA <superscript>+</superscript> domain. Trp quenching studies on VpsR <superscript>R</superscript> , VpsR <superscript>A</superscript> , VpsR <superscript>RA</superscript> , VpsR <superscript>AD</superscript> with c-di-GMP additionally demonstrated that c-di-GMP could potentially bind VpsR <superscript>D</superscript> . We propose that c-di-GMP mediated tethering of VpsR <superscript>D</superscript> with VpsR <superscript>A</superscript> could likely favor generating the specific protein-DNA architecture for transcription activation.<br />Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.<br /> (Copyright © 2021 Elsevier Ltd. All rights reserved.)
- Subjects :
- Adenosine Triphosphatases chemistry
Bacterial Proteins metabolism
Biofilms
Crystallography, X-Ray
Gene Expression Regulation, Bacterial
Models, Molecular
Phosphorylation
Promoter Regions, Genetic
Protein Conformation
Signal Transduction
Vibrio cholerae genetics
Adenosine Triphosphatases metabolism
Binding Sites
Cyclic GMP analogs & derivatives
DNA, Bacterial metabolism
Subjects
Details
- Language :
- English
- ISSN :
- 1089-8638
- Volume :
- 434
- Issue :
- 2
- Database :
- MEDLINE
- Journal :
- Journal of molecular biology
- Publication Type :
- Academic Journal
- Accession number :
- 34774564
- Full Text :
- https://doi.org/10.1016/j.jmb.2021.167354