Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 34499.26 
• Atom Count: 2435 
• Residue Count: 312 
• Unique protein chains: 2

3SNB

Crystal structure of SARS coronavirus main protease complexed with Ac-DSFDQ-H (soaking)

• DOI: 10.2210/pdb3SNB/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human SARS coronavirus
• Expression System: Escherichia coli


• Deposited: 2011-06-29 Released: 2011-09-07 
• Deposition Author(s): Zhu, L., Hilgenfeld, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.250 
• R-Value Work: 0.209 

Literature

Peptide aldehyde inhibitors challenge the substrate specificity of the SARS-coronavirus main protease.

Zhu, L., George, S., Schmidt, M.F., Al-Gharabli, S.I., Rademann, J., Hilgenfeld, R.

(2011) Antiviral Res. 92: 204-212

• PubMed: 21854807 
• DOI: 10.1016/j.antiviral.2011.08.001
• Primary Citation of Related Structures:  
  3SNE, 3SND, 3SNC, 3SNA, 3SN8


• PubMed Abstract: 
  

SARS coronavirus main protease (SARS-CoV M(pro)) is essential for the replication of the virus and regarded as a major antiviral drug target. The enzyme is a cysteine protease, with a catalytic dyad (Cys-145/His-41) in the active site. Aldehyde inhibitors can bind reversibly to the active-site sulfhydryl of SARS-CoV M(pro). Previous studies using peptidic substrates and inhibitors showed that the substrate specificity of SARS-CoV M(pro) requires glutamine in the P1 position and a large hydrophobic residue in the P2 position. We determined four crystal structures of SARS-CoV M(pro) in complex with pentapeptide aldehydes (Ac-ESTLQ-H, Ac-NSFSQ-H, Ac-DSFDQ-H, and Ac-NSTSQ-H). Kinetic data showed that all of these aldehydes exhibit inhibitory activity towards SARS-CoV M(pro), with K(i) values in the μM range. Surprisingly, the X-ray structures revealed that the hydrophobic S2 pocket of the enzyme can accommodate serine and even aspartic-acid side-chains in the P2 positions of the inhibitors. Consequently, we reassessed the substrate specificity of the enzyme by testing the cleavage of 20 different tetradecapeptide substrates with varying amino-acid residues in the P2 position. The cleavage efficiency for the substrate with serine in the P2 position was 160-times lower than that for the original substrate (P2=Leu); furthermore, the substrate with aspartic acid in the P2 position was not cleaved at all. We also determined a crystal structure of SARS-CoV M(pro) in complex with aldehyde Cm-FF-H, which has its P1-phenylalanine residue bound to the relatively hydrophilic S1 pocket of the enzyme and yet exhibits a high inhibitory activity against SARS-CoV M(pro), with K(i)=2.24±0.58 μM. These results show that the stringent substrate specificity of the SARS-CoV M(pro) with respect to the P1 and P2 positions can be overruled by the highly electrophilic character of the aldehyde warhead, thereby constituting a deviation from the dogma that peptidic inhibitors need to correspond to the observed cleavage specificity of the target protease.

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Organizational Affiliation: 

Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
3C-like proteinase	A	306	Human SARS coronavirus	Mutation(s): 0
Find proteins for P0C6U8 (Human SARS coronavirus) Go to UniProtKB:  P0C6U8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Peptide aldehyde inhibitor Ac-DSFDQ-H	H	6	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001118	H	Peptide aldehyde inhibitor Ac-DSFDQ-H	Polypeptide / Enzyme inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.250 
• R-Value Work: 0.209 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 108.740	α = 90.00
b = 81.860	β = 104.26
c = 53.210	γ = 90.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MAR345dtb	data collection
REFMAC	refinement
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-06-29 
• Released Date: 2011-09-07 
• Deposition Author(s): Zhu, L., Hilgenfeld, R.

Revision History 

• Version 1.0: 2011-09-07
  Type: Initial release
• Version 1.1: 2011-09-14
  Type: Structure summary
• Version 1.2: 2011-11-09
  Type: Database references
• Version 1.3: 2012-12-12
  Type: Other