Ca2+-based allosteric switches and shape shifting in RGLG1 VWA domain

Qin Wang; YaYu Chen; ShengPing Li; WenDi Yang; LiFang Sun; MeiQin Jang; XiuLing Wu; QianChao Wang; Lifei Chen; YunKun Wu

doi:10.1016/j.csbj.2020.03.023

Ca²⁺-based allosteric switches and shape shifting in RGLG1 VWA domain

Comput Struct Biotechnol J. 2020 Mar 30:18:821-833. doi: 10.1016/j.csbj.2020.03.023. eCollection 2020.

Authors

Qin Wang^{1

2}, YaYu Chen³, ShengPing Li⁴, WenDi Yang³, LiFang Sun³, MeiQin Jang¹, XiuLing Wu¹, QianChao Wang¹, Lifei Chen³, YunKun Wu³

Affiliations

¹ State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yangqiao West Road, Fuzhou 350002, China.
² University of Chinese Academy of Sciences, Beijing 100049, China.
³ Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou 350117, China.
⁴ Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou 350002 China.

Abstract

RGLG1 is an E3 ubiquitin ligase in Arabidopsis thaliana that participates in ABA signaling and regulates apical dominance. Here, we present crystal structures of RGLG1 VWA domain, revealing two novel calcium ions binding sites (NCBS1 and NCBS2). Furthermore, the structures with guided mutagenesis in NCBS1 prove that Ca²⁺ ions play important roles in controlling conformational change of VWA, which is stabilized in open state with Ca²⁺ bound and converted to closed state after Ca²⁺ removal. This allosteric regulation mechanism is distinct from the ever reported one involving the C-terminal helix in integrin α and β I domains. The mutation of a key residue in NCBS2 do not abolish its Ca²⁺-binding potential, with no conformational change. MD simulations reveals that open state of RGLG1 VWA has higher ligand affinity than its closed state, consisting with integrin. Structural comparison of ion-free-MIDAS with Mg²⁺-MIDAS reveals that Mg²⁺ binding to MIDAS does not induce conformational change. With acquisition of first structure of plant VWA domain in both open state and closed state, we carefully analyze the conformational change and propose a totally new paradigm for its transition of open-closed states, which will be of great value for guiding future researches on VWA proteins and their important biological significance.

Keywords: Calcium ions binding site; Closed state; Conformational change; Molecular dynamics simulation; Open state; VWA domain.