1XT9 image
Deposition Date 2004-10-21
Release Date 2004-12-21
Last Version Date 2024-10-09
Entry Detail
PDB ID:
1XT9
Keywords:
HYDROLASE/HYDROLASE INHIBITOR
Title:
Crystal Structure of Den1 in complex with Nedd8
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.20 Å
R-Value Free:
0.25
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 21 21 2
1XT9 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Sentrin-specific protease 8
Gene (Uniprot):SENP8
Chain IDs:A
Chain Length:212
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q96LD8 Pfam ID:PF02902
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Neddylin
Gene (Uniprot):NEDD8
Chain IDs:B
Chain Length:76
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q15843 Pfam ID:PF00240
Primary Citation
Structure of a Complex between Nedd8 and the Ulp/Senp Protease Family Member Den1.
J.Mol.Biol. 345 141 151 (2005)
PMID: 15567417 DOI: 10.1016/j.jmb.2004.10.022

Abstact

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.

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Primary Citation of related structures
1XT9