1LVO

Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain.

Anand, K.Palm, G.J.Mesters, J.R.Siddell, S.G.Ziebuhr, J.Hilgenfeld, R.

(2002) EMBO J 21: 3213-3224

  • DOI: 10.1093/emboj/cdf327
  • Primary Citation of Related Structures:  
    1LVO

  • PubMed Abstract: 
  • The key enzyme in coronavirus polyprotein processing is the viral main proteinase, M(pro), a protein with extremely low sequence similarity to other viral and cellular proteinases. Here, the crystal structure of the 33.1 kDa transmissible gastroenteritis (corona)virus M(pro) is reported ...

    The key enzyme in coronavirus polyprotein processing is the viral main proteinase, M(pro), a protein with extremely low sequence similarity to other viral and cellular proteinases. Here, the crystal structure of the 33.1 kDa transmissible gastroenteritis (corona)virus M(pro) is reported. The structure was refined to 1.96 A resolution and revealed three dimers in the asymmetric unit. The mutual arrangement of the protomers in each of the dimers suggests that M(pro) self-processing occurs in trans. The active site, comprised of Cys144 and His41, is part of a chymotrypsin-like fold that is connected by a 16 residue loop to an extra domain featuring a novel alpha-helical fold. Molecular modelling and mutagenesis data implicate the loop in substrate binding and elucidate S1 and S2 subsites suitable to accommodate the side chains of the P1 glutamine and P2 leucine residues of M(pro) substrates. Interactions involving the N-terminus and the alpha-helical domain stabilize the loop in the orientation required for trans-cleavage activity. The study illustrates that RNA viruses have evolved unprecedented variations of the classical chymotrypsin fold.


    Related Citations: 
    • Virus-encoded proteinases and proteolytic processing in the Nidovirales
      Ziebuhr, J., Snijder, E.J., Gorbalenya, A.E.
      (2000) J Gen Virol 81: 853

    Organizational Affiliation

    Department of Structural Biology and Crystallography, Institute of Molecular Biotechnology, D-07745 Jena , Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Replicase, hydrolase domainA, B, C, D, E, F302Transmissible gastroenteritis virusMutation(s): 0 
Gene Names: ORF1a
EC: 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
UniProt
Find proteins for P0C6Y5 (Porcine transmissible gastroenteritis coronavirus (strain Purdue))
Explore P0C6Y5 
Go to UniProtKB:  P0C6Y5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MRD
Query on MRD

Download Ideal Coordinates CCD File 
CA [auth C], IA [auth D], O [auth A], PA [auth E], U [auth B], VA [auth F](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
DA [auth D] , EA [auth D] , FA [auth D] , G [auth A] , GA [auth D] , H [auth A] , HA [auth D] , I [auth A] , 
DA [auth D], EA [auth D], FA [auth D], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], J [auth A], JA [auth E], K [auth A], KA [auth E], LA [auth E], MA [auth E], P [auth B], Q [auth B], QA [auth F], R [auth B], RA [auth F], S [auth B], SA [auth F], TA [auth F], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DIO
Query on DIO

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , L [auth A] , M [auth A] , N [auth A] , NA [auth E] , OA [auth E] , T [auth B] , 
AA [auth C], BA [auth C], L [auth A], M [auth A], N [auth A], NA [auth E], OA [auth E], T [auth B], UA [auth F]
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.82α = 90
b = 160.13β = 94.3
c = 88.96γ = 90
Software Package:
Software NamePurpose
SnBphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-17
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description