Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 68996.69 
• Atom Count: 4804 
• Residue Count: 614 
• Unique protein chains: 3

2J7Q

Crystal structure of the ubiquitin-specific protease encoded by murine cytomegalovirus tegument protein M48 in complex with a ubquitin-based suicide substrate

• DOI: 10.2210/pdb2J7Q/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2006-10-16 Released: 2007-03-20 
• Deposition Author(s): Schlieker, C., Weihofen, W.A., Frijns, E., Kattenhorn, L.M., Gaudet, R., Ploegh, H.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.214 
• R-Value Work: 0.156 

Literature

Structure of a Herpesvirus-Encoded Cysteine Protease Reveals a Unique Class of Deubiquitinating Enzymes

Schlieker, C., Weihofen, W.A., Frijns, E., Kattenhorn, L.M., Gaudet, R., Ploegh, H.L.

(2007) Mol.Cell 25: 677

• PubMed: 17349955 
• DOI: 10.1016/j.molcel.2007.01.033


• PubMed Abstract: 
  

All members of the herpesviridae contain within their large tegument protein a cysteine protease module that displays deubiquitinating activity. We report the crystal structure of the cysteine protease domain of murine cytomegalovirus M48 (M48(USP)) in a complex with a ubiquitin (Ub)-based suicide substrate. M48(USP) adopts a papain-like fold, with the active-site cysteine forming a thioether linkage to the suicide substrate. The Ub core participates in an extensive hydrophobic interaction with an exposed beta hairpin loop of M48(USP). This Ub binding mode contributes to Ub specificity and is distinct from that observed in other deubiquitinating enzymes. Both the arrangement of active-site residues and the architecture of the interface with Ub lead us to classify this domain as the founding member of a previously unknown class of deubiquitinating enzymes.

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Organizational Affiliation: 

Department of Biology, Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
MCMV TEGUMENT PROTEIN M48 ENCODED UBIQUITIN- SPECIFIC PROTEASE, M48USP	A	232	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
UBIQUITIN	B, D	75	Homo sapiens	Mutation(s): 0  Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens) Go to Gene View: UBC Go to UniProtKB:  P0CG48

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
MCMV TEGUMENT PROTEIN M48 ENCODED UBIQUITIN- SPECIFIC PROTEASE, M48USP	C	232	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	C	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
PG4	B	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
MG	A, B, D	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
GVE	A, C	METHYL 4-AMINOBUTANOATE C5 H11 N O2 KVQGGLZHHFGHPU-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.214 
• R-Value Work: 0.156 
• Space Group: P 1

Unit Cell:

Length (Å)	Angle (°)
a = 40.907	α = 73.37
b = 57.298	β = 85.37
c = 67.279	γ = 88.54

Software Package:

Software Name	Purpose
HKL2MAP	phasing
HKL-2000	data scaling
REFMAC	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-10-16 
• Released Date: 2007-03-20 
• Deposition Author(s): Schlieker, C., Weihofen, W.A., Frijns, E., Kattenhorn, L.M., Gaudet, R., Ploegh, H.L.

Revision History 

• Version 1.0: 2007-03-20
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Advisory, Version format compliance