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J. Biol. Chem., Vol. 282, Issue 29, 21361-21369, July 20, 2007

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Detailed Structural Insights into the p97-Npl4-Ufd1 Interface^*

Rivka L. Isaacson, Valerie E. Pye, Peter Simpson, Hemmo H. Meyer, Xiaodong Zhang, Paul S. Freemont, and Steve Matthews¹

From the Division of Molecular Biosciences, Imperial College London, Biochemistry Building, South Kensington, London SW7 2AZ, United Kingdom and the Swiss Federal School of Technology (ETH), Institute of Biochemistry, ETH Honggerberg HPM, Zurich 8093, Switzerland

The AAA ATPase, p97, achieves its versatility through binding to a wide range of cofactor proteins that adapt it to different cellular functions. The heterodimer UN (comprising Ufd1 and Npl4) is an adaptor complex that recruits p97 for numerous tasks, many of which involve the ubiquitin pathway. Insights into the structural specificity of p97 for its UN adaptor are currently negligible. Here, we present the solution structure of the Npl4 "ubiquitin-like" domain (UBD), which adopts a -grasp fold with a 3₁₀ helical insert. Moreover we performed a chemical shift perturbation analysis of its binding surface with the p97 N domain. We assigned the backbone amides of the p97 N domain and probed both its reciprocal binding surface with Npl4 UBD and its interaction with the p97-binding region of Ufd1. NMR data recorded on a 400-kDa full-length UN-hexamer p97 complex reveals an identical mode of interaction. We calculated a structural model for the p97 N-Npl4 UBD complex, and a comparison with the p97-p47 adaptor complex reveals subtle differences in p97 adaptor recognition and specificity.

Received for publication, October 27, 2006 , and in revised form, April 11, 2007.

The atomic coordinates and structure factors (code 2PJH) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

^* This work was supported by a grant from the Wellcome Trust. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

¹ To whom correspondence should be addressed. E-mail: s.j.matthews{at}imperial.ac.uk.

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