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Structural basis of NEDD8 ubiquitin discrimination by the deNEDDylating enzyme NEDP1

Lin‐nan Shen, Huanting Liu, Changjiang Dong, Dimitris Xirodimas, James H Naismith, Ronald T Hay

Author Affiliations

  1. Lin‐nan Shen1,,
  2. Huanting Liu1,,
  3. Changjiang Dong1,
  4. Dimitris Xirodimas1,
  5. James H Naismith*,1 and
  6. Ronald T Hay*,1
  1. 1 Centre for Biomolecular Sciences, University of St Andrews, North Haugh, St Andrews, Fife, UK
  1. *Corresponding authors: Centre for Biomolecular Sciences, Biomolecular Science Building, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK. Tel.: +44 1334 463396; Fax: +44 1334 462595; E‐mail: naismith{at}st-and.ac.uk or E‐mail: rth{at}st-and.ac.uk
  1. These authors contributed equally to this work

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Abstract

NEDD8 (neural precursor cell expressed developmentally downregulated gene 8)‐specific protease NEDP1 processes preNEDD8 to its mature form and deconjugates NEDD8 from substrates such as p53 and cullins. Although NEDD8 and ubiquitin are highly related in sequence and structure, their attachment to a protein leads to different biological effects. It is therefore critical that NEDP1 discriminates between NEDD8 and ubiquitin, and this requires remarkable precision in molecular recognition. To determine the basis of this specificity, we have determined the crystal structure of NEDP1 in isolation and in a transition state complex with NEDD8. This reveals that NEDP1 is a cysteine protease of the Ulp family. Binding of NEDD8 induces a dramatic conformational change in a flexible loop that swings over the C‐terminus of NEDD8 locking it into an extended β‐structure optimal for catalysis. Structural, mutational and biochemical studies have identified key residues involved in molecular recognition. A single‐residue difference in the C‐terminus of NEDD8 and ubiquitin contributes significantly to the ability of NEDP1 to discriminate between them. In vivo analysis indicates that NEDP1 mutants perturb deNEDDylation of the tumour suppressor p53.

  • Received December 24, 2004.
  • Accepted February 23, 2005.
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