1XT9

Crystal Structure of Den1 in complex with Nedd8

Summary for 1XT9

• Entry DOI: 10.2210/pdb1xt9/pdb
• Descriptor: Sentrin-specific protease 8, Neddylin (3 entities in total)
• Functional Keywords: cysteine protease, ubiquitin-like, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: Q15843
• Total number of polymer chains: 2
• Total formula weight: 32707.26

Authors

Reverter, D.,Wu, K.,Erdene, T.G.,Pan, Z.Q.,Wilkinson, K.D.,Lima, C.D. (deposition date: 2004-10-21, release date: 2004-12-21, Last modification date: 2024-10-09)

Primary citation

Reverter, D.,Wu, K.,Erdene, T.G.,Pan, Z.Q.,Wilkinson, K.D.,Lima, C.D.
Structure of a Complex between Nedd8 and the Ulp/Senp Protease Family Member Den1.
J.Mol.Biol., 345:141-151, 2005

PubMed Abstract: The Nedd8 conjugation pathway is conserved from yeast to humans and is essential in many organisms. Nedd8 is conjugated to cullin proteins in a process that alters SCF E3 ubiquitin ligase activity, and it is presumed that Nedd8 deconjugation would reverse these effects. We now report the X-ray structures of the human Nedd8-specific protease, Den1, in a complex with the inhibitor Nedd8 aldehyde, thus revealing a model for the tetrahedral transition state intermediate generated during proteolysis. Although Den1 is closely related to the SUMO-specific protease family (Ulp/Senp family), structural analysis of the interface suggests determinants involved in Nedd8 selectivity by Den1 over other ubiquitin-like family members and suggests how the Ulp/Senp architecture has been modified to interact with different ubiquitin-like modifiers.

PubMed: 15567417
DOI: 10.1016/j.jmb.2004.10.022

Experimental method

X-RAY DIFFRACTION (2.2 Å)