2IPH

X-ray Structure at 1.75 A Resolution of a Norovirus Protease Linked to an Active Site Directed Peptide Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Structural Study of Norovirus 3C Protease Specificity: Binding of a Designed Active Site-Directed Peptide Inhibitor.

Hussey, R.J.Coates, L.Gill, R.S.Erskine, P.T.Coker, S.F.Mitchell, E.Cooper, J.B.Wood, S.Broadbridge, R.Clarke, I.N.Lambden, P.R.Shoolingin-Jordan, P.M.

(2011) Biochemistry 50: 240-249

  • DOI: 10.1021/bi1008497
  • Primary Citation of Related Structures:  
    2IPH

  • PubMed Abstract: 
  • Noroviruses are the major cause of human epidemic nonbacterial gastroenteritis. Viral replication requires a 3C cysteine protease that cleaves a 200 kDa viral polyprotein into its constituent functional proteins. Here we describe the X-ray structure of the Southampton norovirus 3C protease (SV3CP) bound to an active site-directed peptide inhibitor (MAPI) which has been refined at 1 ...

    Noroviruses are the major cause of human epidemic nonbacterial gastroenteritis. Viral replication requires a 3C cysteine protease that cleaves a 200 kDa viral polyprotein into its constituent functional proteins. Here we describe the X-ray structure of the Southampton norovirus 3C protease (SV3CP) bound to an active site-directed peptide inhibitor (MAPI) which has been refined at 1.7 Å resolution. The inhibitor, acetyl-Glu-Phe-Gln-Leu-Gln-X, which is based on the most rapidly cleaved recognition sequence in the 200 kDa polyprotein substrate, reacts covalently through its propenyl ethyl ester group (X) with the active site nucleophile, Cys 139. The structure permits, for the first time, the identification of substrate recognition and binding groups in a noroviral 3C protease and thus provides important new information for the development of antiviral prophylactics.


    Organizational Affiliation

    School of Biological Sciences, University of Southampton, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thiol protease P3CA, B181Southampton virus (serotype 3)Mutation(s): 0 
Gene Names: ORF1
EC: 3.4.22 (PDB Primary Data), 3.6.1.15 (UniProt), 3.4.22.66 (UniProt), 2.7.7.48 (UniProt)
Find proteins for Q04544 (Southampton virus (strain GI/Human/United Kingdom/Southampton/1991))
Explore Q04544 
Go to UniProtKB:  Q04544
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LGG
Query on LGG

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]N-ACETYL-L-ALPHA-GLUTAMYL-L-PHENYLALANYL-L-GLUTAMINYL-N-[(1S)-4-AMINO-1-(2-CARBOXYETHYL)-4-OXOBUTYL]-L-LEUCINAMIDE
C34 H51 N7 O11
IDWPNCOZKNRFJZ-LROMGURASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.497α = 90
b = 84.106β = 90
c = 121.471γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
SOLVEphasing
RESOLVEphasing
CNSrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2006-10-12 
  • Released Date: 2007-10-23 
  • Deposition Author(s): Hussey, R.J.

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-06-20
    Changes: Database references