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Structural basis for Ca2+-induced activation of human PAD4

Nature Structural & Molecular Biology volume 11, pages 777–783 (2004)Cite this article

Abstract

Peptidylarginine deiminase 4 (PAD4) is a Ca2+-dependent enzyme that catalyzes the conversion of protein arginine residues to citrulline. Its gene is a susceptibility locus for rheumatoid arthritis. Here we present the crystal structure of Ca2+-free wild-type PAD4, which shows that the polypeptide chain adopts an elongated fold in which the N-terminal domain forms two immunoglobulin-like subdomains, and the C-terminal domain forms an α/β propeller structure. Five Ca2+-binding sites, none of which adopt an EF-hand motif, were identified in the structure of a Ca2+-bound inactive mutant with and without bound substrate. These structural data indicate that Ca2+ binding induces conformational changes that generate the active site cleft. Our findings identify a novel mechanism for enzyme activation by Ca2+ ions, and are important for understanding the mechanism of protein citrullination and for developing PAD-inhibiting drugs for the treatment of rheumatoid arthritis.

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Figure 1: Overall structure of PAD4.
Figure 2: Structure of the C-terminal domain in PAD4.
Figure 3: Structure of the substrate- and Ca2+-binding sites in PAD4.
Figure 4: Electrostatic surface potentials of Ca2+-free PAD4 (left), Ca2+-bound PAD4 (middle) and the substrate complex (right).
Figure 5

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Acknowledgements

The authors thank M.Y., T.K. and K.M. for data collection at SPring-8 and N.M., N.I., M.S. and S.W. for data collection at PF-AR. This work was supported by grants-in-aid for young scientists (B) from the Japan Society of the Promotion of Science (JSPS) to H.H. (14780515), grants-in-aid for scientific research (C) from the JSPS to T.S. (15570101) and M.Y. (15570122), and by the Japan Ministry of Education, Culture, Sports, Science and Technology Project on Protein Structural and Functional Analyses.

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  1. Graduate School of Integrated Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan

    Kyouhei Arita, Hiroshi Hashimoto, Toshiyuki Shimizu & Mamoru Sato

  2. Graduate School of Integrated Science, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, 236-0027, Japan

    Katsuhiko Nakashima & Michiyuki Yamada

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  1. Kyouhei Arita
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Correspondence to Mamoru Sato.

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Supplementary Fig. 1

Multiple sequence alignment of human PADs. (PDF 731 kb)

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Arita, K., Hashimoto, H., Shimizu, T. et al. Structural basis for Ca2+-induced activation of human PAD4. Nat Struct Mol Biol 11, 777–783 (2004). https://doi.org/10.1038/nsmb799

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