7V4E

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

7V4E の概要

• エントリーDOI: 10.2210/pdb7v4e/pdb
• 分子名称: VpsR, SULFATE ION, 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) (3 entities in total)
• 機能のキーワード: x-ray crystallography; biofilm; fluorescence quenching; atpase activity; second-messenger, transcription
• 由来する生物種: Vibrio cholerae
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 91017.17

構造登録者

Chakrabortty, T.,Sen, U. (登録日: 2021-08-12, 公開日: 2022-04-06, 最終更新日: 2023-11-29)

主引用文献

Chakrabortty, T.,Roy Chowdhury, S.,Ghosh, B.,Sen, U.
Crystal Structure of VpsR Revealed Novel Dimeric Architecture and c-di-GMP Binding Site: Mechanistic Implications in Oligomerization, ATPase Activity and DNA Binding.
J.Mol.Biol., 434:167354-167354, 2022

PubMed Abstract: VpsR, the master regulator of biofilm formation in Vibrio cholerae, is an atypical NtrC1 type bEBP lacking residues essential for σ-RNAP binding and REC domain phosphorylation. Moreover, transcription from P, a promoter of biofilm biosynthesis, has been documented in presence of σ-RNAP/VpsR/c-di-GMP complex. It was proposed that c-di-GMP and VpsR together form an active transcription complex with σ-RNAP. However, the impact of c-di-GMP imparted on VpsR that leads to transcription activation with σ-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, containing REC and AAA domains, in apo, AMPPNP/GMPPNP and c-di-GMP bound states. Structures of VpsR 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 complex reveals that c-di-GMP binds near the C-terminal end of AAA domain. Trp quenching studies on VpsR, VpsR, VpsR, VpsR with c-di-GMP additionally demonstrated that c-di-GMP could potentially bind VpsR. We propose that c-di-GMP mediated tethering of VpsR with VpsR could likely favor generating the specific protein-DNA architecture for transcription activation.

PubMed: 34774564
DOI: 10.1016/j.jmb.2021.167354

実験手法

X-RAY DIFFRACTION (4 Å)