2J7Q | pdb_00002j7q

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

PDB DOI: https://doi.org/10.2210/pdb2J7Q/pdb

Classification: HYDROLASE
Organism(s): Murid betaherpesvirus 1, Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.214 (Depositor), 0.226 (DCC)
R-Value Work:
0.156 (Depositor), 0.167 (DCC)
R-Value Observed:
0.157 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.molcel.2007.01.033
Primary Citation Related Structures:
2J7Q

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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 69 kDa
Atom Count: 5,511
Modeled Residue Count: 614
Deposited Residue Count: 614
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MCMV TEGUMENT PROTEIN M48 ENCODED UBIQUITIN- SPECIFIC PROTEASE, M48USP	A	232	Murid betaherpesvirus 1	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN	B, D	75	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48 Go to UniProtKB: P0CG48
PHAROS: P0CG48 GTEx: ENSG00000150991
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CG48
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MCMV TEGUMENT PROTEIN M48 ENCODED UBIQUITIN- SPECIFIC PROTEASE, M48USP	C	232	Murid betaherpesvirus 1	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
GVE Query on GVE Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain F [auth A]	F [auth A], J [auth C]	METHYL 4-AMINOBUTANOATE C₅ H₁₁ N O₂ KVQGGLZHHFGHPU-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.214 (Depositor), 0.226 (DCC)
R-Value Work: 0.156 (Depositor), 0.167 (DCC)
R-Value Observed: 0.157 (Depositor)

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
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL2Map	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-03-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-03-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description