PDBsum entry: 2gfo

Hydrolase

PDB id: 2gfo

Contents

Protein chain

339 a.a. *

Metals

_ZN

Waters ×191

* Residue conservation analysis

PDB id:

2gfo

Name:

Hydrolase

Title:

Structure of the catalytic domain of human ubiquitin carboxy hydrolase 8

Structure:

Ubiquitin carboxyl-terminal hydrolase 8. Chain: a. Fragment: catalytic domain. Synonym: ubiquitin thiolesterase 8, ubiquitin-specific proc protease 8, deubiquitinating enzyme 8, hubpy. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: usp8, kiaa0055, ubpy. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

2.00Å R-factor: 0.171 R-free: 0.210

Authors:

J.R.Walker,G.V Avvakumov,S.Xue,E.M.Newman,P.J.Finerty Jr.,C. Cole,J.Weigelt,M.Sundstrom,C.Arrowsmith,A.Edwards,A.Bochkar Paganon,Structural Genomics Consortium (Sgc)

Key ref:

G.V.Avvakumov et al. (2006). Amino-terminal dimerization, NRDP1-rhodanese interaction, and inhibited catalytic domain conformation of the ubiquitin-specific protease 8 (USP8). J Biol Chem, 281, 38061-38070. PubMed id: 17035239 DOI: 10.1074/jbc.M606704200

Date:

22-Mar-06 Release date: 04-Apr-06

Protein chain

P40818  (UBP8_HUMAN) -  Ubiquitin carboxyl-terminal hydrolase 8

Seq: 1118 a.a.

Struc: 339 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.19.12 - Ubiquitinyl hydrolase 1.
• Reaction: Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).

 Gene Ontology (GO) functional annotation 

• Biological process: ubiquitin-dependent protein catabolic process (1 term)
• Biochemical function: ubiquitin thiolesterase activity (1 term)

DOI no: 10.1074/jbc.M606704200

J Biol Chem 281:38061-38070 (2006)

PubMed id: 17035239

Amino-terminal dimerization, NRDP1-rhodanese interaction, and inhibited catalytic domain conformation of the ubiquitin-specific protease 8 (USP8).

G.V.Avvakumov, J.R.Walker, S.Xue, P.J.Finerty, F.Mackenzie, E.M.Newman, S.Dhe-Paganon.

ABSTRACT

Ubiquitin-specific protease 8 (USP8) hydrolyzes mono and polyubiquitylated targets such as epidermal growth factor receptors and is involved in clathrin-mediated internalization. In 1182 residues, USP8 contains multiple domains, including coiled-coil, rhodanese, and catalytic domains. We report the first high-resolution crystal structures of these domains and discuss their implications for USP8 function. The amino-terminal domain is a homodimer with a novel fold. It is composed of two five-helix bundles, where the first helices are swapped, and carboxyl-terminal helices are extended in an antiparallel fashion. The structure of the rhodanese domain, determined in complex with the E3 ligase NRDP1, reveals the canonical rhodanese fold but with a distorted primordial active site. The USP8 recognition domain of NRDP1 has a novel protein fold that interacts with a conserved peptide loop of the rhodanese domain. A consensus sequence of this loop is found in other NRDP1 targets, suggesting a common mode of interaction. The structure of the carboxyl-terminal catalytic domain of USP8 exhibits the conserved tripartite architecture but shows unique traits. Notably, the active site, including the ubiquitin binding pocket, is in a closed conformation, incompatible with substrate binding. The presence of a zinc ribbon subdomain near the ubiquitin binding site further suggests a polyubiquitin-specific binding site and a mechanism for substrate induced conformational changes.

Selected figure(s)

Figure 3.
FIGURE 3. Structure and coordination of the Usp8 rhodanese loop. a, electrostatic surface representation (-10 kt/e, red to +10 kt/e, blue) of NRDP1 was generated by the APBS software package and displayed in Pymol. Active site residues of NRDP1 are in green. b, detailed protein-protein interactions between USP8 and NRDP1. The bound USP8 peptide is shown in purple and the peptide binding site of Nrdp1 in orange. Hydrogen bonds are shown as dashed lines, and non-ligand residues involved in hydrophobic contacts are shown as rising sun. Data and image were generated with LigPlot.

Figure 5.
FIGURE 5. Stereo representation of the USP8 active site and conformation of BL1 and BL2. a, USP8 is shown as ribbon representation with the same color scheme as described in the legend to Fig. 4, showing the closed BL2 conformation and an active site that is filled. The catalytic triad is shown as stick representation (Cys-786, His-1067, and Asp-1084). Two water or chloride molecules are shown as small spheres, one in the oxyanion pocket and the other in the P2 position. Hydrogen bonds are labeled as black dashed lines, and their distances are marked. All non-hydrogen atoms of the BL2 loop are shown. b, BL1 and BL2 conformations of USP7 (green), USP8 (brown), and USP14 (red) are shown in ribbon format, showing the closed orientations. The BL2 loop of USP7 is not visible because of high flexibility.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 38061-38070) copyright 2006.

Figures were selected by an automated process.