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

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thiol protease P3C
A, B
181Southampton virus (strain GI/Human/United Kingdom/Southampton/1991)Mutation(s): 0 
Find proteins for Q04544 (Southampton virus (strain GI/Human/United Kingdom/Southampton/1991))
Go to UniProtKB:  Q04544
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LGG
Query on LGG

Download SDF File 
Download CCD File 
A, 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 = 90.00
b = 84.106β = 90.00
c = 121.471γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
RESOLVEphasing
SCALAdata scaling
MOSFLMdata reduction
SOLVEphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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