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PDBsum entry 2bx4

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protein links
Hydrolase PDB id
2bx4
Jmol
Contents
Protein chain
298 a.a. *
Waters ×46
* Residue conservation analysis
PDB id:
2bx4
Name: Hydrolase
Title: Crystal structure of sars coronavirus main proteinase (p21212)
Structure: 3c-like proteinase. Chain: a. Fragment: residues 3241-3546. Synonym: main proteinase, 3cl-pro, 3clp, nsp5. Engineered: yes
Source: Sars coronavirus sin2774. Organism_taxid: 235410. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.79Å     R-factor:   0.221     R-free:   0.302
Authors: K.H.G.Verschueren,J.R.Mesters,J.Bigalke,R.Hilgenfeld
Key ref:
J.Tan et al. (2005). pH-dependent conformational flexibility of the SARS-CoV main proteinase (M(pro)) dimer: molecular dynamics simulations and multiple X-ray structure analyses. J Mol Biol, 354, 25-40. PubMed id: 16242152 DOI: 10.1016/j.jmb.2005.09.012
Date:
22-Jul-05     Release date:   26-Sep-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0C6U8  (R1A_CVHSA) -  Replicase polyprotein 1a
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4382 a.a.
298 a.a.
Protein chain
Pfam   ArchSchema ?
P0C6X7  (R1AB_CVHSA) -  Replicase polyprotein 1ab
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7073 a.a.
298 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.3.4.19.12  - Ubiquitinyl hydrolase 1.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
   Enzyme class 3: E.C.3.4.22.69  - Sars coronavirus main proteinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     viral protein processing   1 term 
  Biochemical function     catalytic activity     1 term  

 

 
DOI no: 10.1016/j.jmb.2005.09.012 J Mol Biol 354:25-40 (2005)
PubMed id: 16242152  
 
 
pH-dependent conformational flexibility of the SARS-CoV main proteinase (M(pro)) dimer: molecular dynamics simulations and multiple X-ray structure analyses.
J.Tan, K.H.Verschueren, K.Anand, J.Shen, M.Yang, Y.Xu, Z.Rao, J.Bigalke, B.Heisen, J.R.Mesters, K.Chen, X.Shen, H.Jiang, R.Hilgenfeld.
 
  ABSTRACT  
 
The SARS coronavirus main proteinase (M(pro)) is a key enzyme in the processing of the viral polyproteins and thus an attractive target for the discovery of drugs directed against SARS. The enzyme has been shown by X-ray crystallography to undergo significant pH-dependent conformational changes. Here, we assess the conformational flexibility of the M(pro) by analysis of multiple crystal structures (including two new crystal forms) and by molecular dynamics (MD) calculations. The MD simulations take into account the different protonation states of two histidine residues in the substrate-binding site and explain the pH-activity profile of the enzyme. The low enzymatic activity of the M(pro) monomer and the need for dimerization are also discussed.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structure of the (a) monomer and (b) dimer of SARS-CoV Mpro. (a) Domains I (light blue) and II (green) each contain a six-stranded b-barrel and domain III (orange) is composed mainly of a-helices. The amino and the carboxy terminus are marked by a blue and an orange sphere, respectively. The flexible loops L1, L2, and L3 (red) comprise residues 138-145 (the oxyanion-binding loop), 165-172, and 185-200, respectively. (b) a-Helices are red and b-strands are light blue. The amino and the carboxy termini are marked by blue and orange spheres, respectively. Dimerization is mainly due to interactions between the helical domains III of each monomer (top). (c) Superimposition (in stereo) of the C^a backbone as determined in three different crystal forms. Blue, monoclinic form; red, tetragonal form; green, orthorhombic form. (a) and (b) were prepared by MOLSCRIPT,40 (c) was prepared by PyMOL.41
Figure 8.
Figure 8. Some characteristic distances in the MD simulations of the SARS-CoV Mpro dimer at (a) pH 6.0, (b) pH 7.6, (c) pH 8.0, and (d) pH 5.0. For each simulation, the distance between Glu166 and His163, Glu166 and His172, Glu166 and Ser1(N) of the other monomer in the dimer, and Phe140 (center of mass of phenyl ring) and His163 (center of mass of imidazole ring) are shown. The shorter of the two distances to the carboxylate oxygen atoms of Glu166, Oe1 and Oe2, is displayed. Green, monomer A; blue, monomer B.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 354, 25-40) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19436709 J.Tan, C.Vonrhein, O.S.Smart, G.Bricogne, M.Bollati, Y.Kusov, G.Hansen, J.R.Mesters, C.L.Schmidt, and R.Hilgenfeld (2009).
The SARS-Unique Domain (SUD) of SARS Coronavirus Contains Two Macrodomains That Bind G-Quadruplexes.
  PLoS Pathog, 5, e1000428.
PDB codes: 2w2g 2wct
17931870 C.Niu, J.Yin, J.Zhang, J.C.Vederas, and M.N.James (2008).
Molecular docking identifies the binding of 3-chloropyridine moieties specifically to the S1 pocket of SARS-CoV Mpro.
  Bioorg Med Chem, 16, 293-302.  
18305031 J.Shi, J.Sivaraman, and J.Song (2008).
Mechanism for controlling the dimer-monomer switch and coupling dimerization to catalysis of the severe acute respiratory syndrome coronavirus 3C-like protease.
  J Virol, 82, 4620-4629.
PDB code: 2qcy
18305043 N.Zhong, S.Zhang, P.Zou, J.Chen, X.Kang, Z.Li, C.Liang, C.Jin, and B.Xia (2008).
Without its N-finger, the main protease of severe acute respiratory syndrome coronavirus can form a novel dimer through its C-terminal domain.
  J Virol, 82, 4227-4234.  
17397959 R.L.Graham, J.S.Sparks, L.D.Eckerle, A.C.Sims, and M.R.Denison (2008).
SARS coronavirus replicase proteins in pathogenesis.
  Virus Res, 133, 88.  
17977841 S.Chen, T.Hu, J.Zhang, J.Chen, K.Chen, J.Ding, H.Jiang, and X.Shen (2008).
Mutation of Gly-11 on the dimer interface results in the complete crystallographic dimer dissociation of severe acute respiratory syndrome coronavirus 3C-like protease: crystal structure with molecular dynamics simulations.
  J Biol Chem, 283, 554-564.
PDB code: 2pwx
18611220 U.Bacha, J.Barrila, S.B.Gabelli, Y.Kiso, L.Mario Amzel, and E.Freire (2008).
Development of broad-spectrum halomethyl ketone inhibitors against coronavirus main protease 3CL(pro).
  Chem Biol Drug Des, 72, 34-49.
PDB code: 3d62
17428870 E.F.Donaldson, R.L.Graham, A.C.Sims, M.R.Denison, and R.S.Baric (2007).
Analysis of murine hepatitis virus strain A59 temperature-sensitive mutant TS-LA6 suggests that nsp10 plays a critical role in polyprotein processing.
  J Virol, 81, 7086-7098.  
17142288 H.P.Chang, C.Y.Chou, and G.G.Chang (2007).
Reversible unfolding of the severe acute respiratory syndrome coronavirus main protease in guanidinium chloride.
  Biophys J, 92, 1374-1383.  
17202208 M.S.Almeida, M.A.Johnson, T.Herrmann, M.Geralt, and K.Wüthrich (2007).
Novel beta-barrel fold in the nuclear magnetic resonance structure of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus.
  J Virol, 81, 3151-3161.
PDB codes: 2gdt 2hsx
16565086 H.Chen, P.Wei, C.Huang, L.Tan, Y.Liu, and L.Lai (2006).
Only one protomer is active in the dimer of SARS 3C-like proteinase.
  J Biol Chem, 281, 13894-13898.  
17154528 J.Barrila, U.Bacha, and E.Freire (2006).
Long-range cooperative interactions modulate dimerization in SARS 3CLpro.
  Biochemistry, 45, 14908-14916.  
17085042 J.R.Mesters, J.Tan, and R.Hilgenfeld (2006).
Viral enzymes.
  Curr Opin Struct Biol, 16, 776-786.  
16688706 S.I.Al-Gharabli, S.T.Shah, S.Weik, M.F.Schmidt, J.R.Mesters, D.Kuhn, G.Klebe, R.Hilgenfeld, and J.Rademann (2006).
An efficient method for the synthesis of peptide aldehyde libraries employed in the discovery of reversible SARS coronavirus main protease (SARS-CoV Mpro) inhibitors.
  Chembiochem, 7, 1048-1055.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.