Structures of human peptidylarginine deiminase type III provide insights into substrate recognition and inhibitor design

Kazumasa Funabashi; Mizuki Sawata; Anna Nagai; Megumi Akimoto; Ryutaro Mashimo; Hidenari Takahara; Kenji Kizawa; Paul R Thompson; Kenji Ite; Kenichi Kitanishi; Masaki Unno

doi:10.1016/j.abb.2021.108911

Structures of human peptidylarginine deiminase type III provide insights into substrate recognition and inhibitor design

Arch Biochem Biophys. 2021 Sep 15:708:108911. doi: 10.1016/j.abb.2021.108911. Epub 2021 May 7.

Authors

Affiliations

¹ Graduate School of Science and Engineering, Ibaraki University, Hitachi, Japan.
² Graduate School of Science and Engineering, Ibaraki University, Hitachi, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai Naka, Japan.
³ Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai Naka, Japan; College of Agriculture, Ibaraki University, Ami Inashiki, Japan.
⁴ Kao Corporation, Biological Science Research Laboratory, Odawara, Japan.
⁵ Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
⁶ Graduate School of Science and Engineering, Ibaraki University, Hitachi, Japan; Tokyo University of Science, Faculty of Science Division I, Tokyo, Japan.
⁷ Graduate School of Science and Engineering, Ibaraki University, Hitachi, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai Naka, Japan. Electronic address: masaki.unno.19@vc.ibaraki.ac.jp.

PMID: 33971157
DOI: 10.1016/j.abb.2021.108911

Abstract

Peptidylarginine deiminase type III (PAD3) is an isozyme belonging to the PAD enzyme family that converts arginine to citrulline residue(s) within proteins. PAD3 is expressed in most differentiated keratinocytes of the epidermis and hair follicles, while S100A3, trichohyalin, and filaggrin are its principal substrates. In this study, the X-ray crystal structures of PAD3 in six states, including its complex with the PAD inhibitor Cl-amidine, were determined. This structural analysis identified a large space around Gly374 in the PAD3-Ca²⁺-Cl-amidine complex, which may be used to develop novel PAD3-selective inhibitors. In addition, similarities between PAD3 and PAD4 were found based on the investigation of PAD4 reactivity with S100A3 in vitro. A comparison of the structures of PAD1, PAD2, PAD3, and PAD4 implied that the flexibility of the structures around the active site may lead to different substrate selectivity among these PAD isozymes.

Keywords: Citrulline; Inhibitor; Isozyme; Post-translational modification; Quaternary structure; Selectivity.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Crystallography, X-Ray
Drug Design*
Enzyme Inhibitors / pharmacology*
Filaggrin Proteins
Humans
Models, Molecular
Protein Binding
Protein Conformation
Protein-Arginine Deiminase Type 3 / antagonists & inhibitors
Protein-Arginine Deiminase Type 3 / chemistry*
Protein-Arginine Deiminase Type 3 / metabolism*

Substances

Enzyme Inhibitors
FLG protein, human
Filaggrin Proteins
Protein-Arginine Deiminase Type 3