5V1Q

Crystal structure of Streptococcus suis SuiB

5V1Q の概要

• エントリーDOI: 10.2210/pdb5v1q/pdb
• 関連するPDBエントリー: 5V1S 5V1T
• 分子名称: Radical SAM, IRON/SULFUR CLUSTER (3 entities in total)
• 機能のキーワード: radical sam enzyme, lys-trp crosslink, streptococcus suis, metalloenzyme, spasm domain, rre domain, metal binding protein
• 由来する生物種: Streptococcus suis
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 108199.31

構造登録者

Davis, K.M.,Bacik, J.P.,Ando, N. (登録日: 2017-03-02, 公開日: 2017-08-30, 最終更新日: 2024-03-06)

主引用文献

Davis, K.M.,Schramma, K.R.,Hansen, W.A.,Bacik, J.P.,Khare, S.D.,Seyedsayamdost, M.R.,Ando, N.
Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition.
Proc. Natl. Acad. Sci. U.S.A., 114:10420-10425, 2017

PubMed Abstract: Posttranslational modification of ribosomally synthesized peptides provides an elegant means for the production of biologically active molecules known as RiPPs (ribosomally synthesized and posttranslationally modified peptides). Although the leader sequence of the precursor peptide is often required for turnover, the exact mode of recognition by the modifying enzymes remains unclear for many members of this class of natural products. Here, we have used X-ray crystallography and computational modeling to examine the role of the leader peptide in the biosynthesis of a homolog of streptide, a recently identified peptide natural product with an intramolecular lysine-tryptophan cross-link, which is installed by the radical -adenosylmethionine (SAM) enzyme, StrB. We present crystal structures of SuiB, a close ortholog of StrB, in various forms, including apo SuiB, SAM-bound SuiB, and a complex of SuiB with SAM and its peptide substrate, SuiA. Although the N-terminal domain of SuiB adopts a typical RRE (RiPP recognition element) motif, which has been implicated in precursor peptide recognition, we observe binding of the leader peptide in the catalytic barrel rather than the N-terminal domain. Computational simulations support a mechanism in which the leader peptide guides posttranslational modification by positioning the cross-linking residues of the precursor peptide within the active site. Together the results shed light onto binding of the precursor peptide and the associated conformational changes needed for the formation of the unique carbon-carbon cross-link in the streptide family of natural products.

PubMed: 28893989
DOI: 10.1073/pnas.1703663114

実験手法

X-RAY DIFFRACTION (2.5 Å)