4I1A

Crystal Structure of the Apo Form of RapI

4I1A の概要

• エントリーDOI: 10.2210/pdb4i1a/pdb
• 関連するPDBエントリー: 3Q15 3ULQ 4GYO
• 分子名称: Response regulator aspartate phosphatase I, CHLORIDE ION (3 entities in total)
• 機能のキーワード: tetratricopeptide repeat, phosphatase, spo0f, hydrolase
• 由来する生物種: Bacillus subtilis subsp. subtilis
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 93320.99

構造登録者

Parashar, V.,Jeffrey, P.D.,Neiditch, M.B. (登録日: 2012-11-20, 公開日: 2013-04-03, 最終更新日: 2024-02-28)

主引用文献

Parashar, V.,Jeffrey, P.D.,Neiditch, M.B.
Conformational change-induced repeat domain expansion regulates rap phosphatase quorum-sensing signal receptors.
Plos Biol., 11:e1001512-e1001512, 2013

PubMed Abstract: The large family of Gram-positive quorum-sensing receptors known as the RNPP proteins consists of receptors homologous to the Rap, NprR, PlcR, and PrgX proteins that are regulated by imported oligopeptide autoinducers. Rap proteins are phosphatases and transcriptional anti-activators, and NprR, PlcR, and PrgX proteins are DNA binding transcription factors. Despite their obvious importance, the mechanistic basis of oligopeptide receptor regulation is largely unknown. Here, we report the X-ray crystal structure of the Bacillus subtilis quorum-sensing receptor RapJ in complex with the centrally important oligopeptide autoinducer competence and sporulation factor (CSF, also termed PhrC), a member of the Phr family of quorum-sensing signals. Furthermore, we present the crystal structure of RapI. Comparison of the RapJ-PhrC, RapI, RapH-Spo0F, and RapF-ComA(C) crystal structures reveals the mechanistic basis of Phr activity. More specifically, when complexed with target proteins, Rap proteins consist of a C-terminal tetratricopeptide repeat (TPR) domain connected by a flexible helix-containing linker to an N-terminal 3-helix bundle. In the absence of a target protein or regulatory peptide, the Rap protein 3-helix bundle adopts different conformations. However, in the peptide-bound conformation, the Rap protein N-terminal 3-helix bundle and linker undergo a radical conformational change, form TPR-like folds, and merge with the existing C-terminal TPR domain. To our knowledge, this is the first example of conformational change-induced repeat domain expansion. Furthermore, upon Phr binding, the entire Rap protein is compressed along the TPR superhelical axis, generating new intramolecular contacts that lock the Rap protein in an inactive state. The fact that Rap proteins are conformationally flexible is surprising considering that it is accepted dogma that TPR proteins do not undergo large conformational changes. Repeat proteins are widely used as scaffolds for the development of designed affinity reagents, and we propose that Rap proteins could be used as scaffolds for engineering novel ligand-switchable affinity reagents.

PubMed: 23526881
DOI: 10.1371/journal.pbio.1001512

実験手法

X-RAY DIFFRACTION (2.443 Å)