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C-terminal domain of SARS-CoV main protease can form a 3D domain-swapped dimer

  1. Nan Zhong1,2,†,
  2. Shengnan Zhang1,2,†,
  3. Fei Xue3,†,
  4. Xue Kang1,2,
  5. Peng Zou1,2,
  6. Jiaxuan Chen1,4,
  7. Chao Liang1,
  8. Zihe Rao3,
  9. Changwen Jin1,2,4,
  10. Zhiyong Lou3,*,
  11. Bin Xia1,2,4,*

Article first published online: 10 FEB 2009

DOI: 10.1002/pro.76

Issue

Protein Science

Protein Science

Volume 18, Issue 4, pages 839–844, April 2009

Additional Information

How to Cite

Zhong, N., Zhang, S., Xue, F., Kang, X., Zou, P., Chen, J., Liang, C., Rao, Z., Jin, C., Lou, Z. and Xia, B. (2009), C-terminal domain of SARS-CoV main protease can form a 3D domain-swapped dimer. Protein Science, 18: 839–844. doi: 10.1002/pro.76

Author Information

  1. 1

    Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, People' Republic of China

  2. 2

    College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People' Republic of China

  3. 3

    Structural Biology Laboratory, Tsinghua University, Beijing 100084, China

  4. 4

    College of Life Science, Peking University, Beijing 100871, People' Republic of China

  1. †

    Nan Zhong, Shengnan Zhang, and Fei Xue authors contributed equally to the work.

*Laboratory of Structural Biology, Tsinghua University, Beijing 100084, People's Republic of China

Publication History

  1. Issue published online: 25 MAR 2009
  2. Article first published online: 10 FEB 2009
  3. Accepted manuscript online: 10 FEB 2009 12:00AM EST
  4. Manuscript Accepted: 15 JAN 2009
  5. Manuscript Revised: 8 JAN 2009
  6. Manuscript Received: 20 NOV 2008

Funded by

  • 973 Program. Grant Number: 2003CB514104
  • NSFC. Grant Number: 30125009
  • 863 Program. Grant Number: 2006AA02A323

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References

  • 1
    Chan HL, Tsui SK, Sung JJ ( 2003) Coronavirus in severe acute respiratory syndrome (SARS). Trends Mol Med 9: 323–325.
  • 2
    Kuiken T, Fouchier RA, Schutten M, Rimmelzwaan GF, van Amerongen G, van Riel D, Laman JD, de Jong T, van Doornum G, Lim W, Ling AE, Chan PK, Tam JS, Zambon MC, Gopal R, Drosten C, van der Werf S, Escriou N, Manuguerra JC, Stohr K, Peiris JS, Osterhaus AD ( 2003) Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome. Lancet 362: 263–270.
  • 3
    Leng Q, Bentwich Z ( 2003) A novel coronavirus and SARS. N Engl J Med 349: 709.
  • 4
    Snijder EJ, Bredenbeek PJ, Dobbe JC, Thiel V, Ziebuhr J, Poon LL, Guan Y, Rozanov M, Spaan WJ, Gorbalenya AE ( 2003) Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. J Mol Biol 331: 991–1004.
  • 5
    Anand K, Ziebuhr J, Wadhwani P, Mesters JR, Hilgenfeld R ( 2003) Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs. Science 300: 1763–1767.
  • 6
    Yang H, Yang M, Ding Y, Liu Y, Lou Z, Zhou Z, Sun L, Mo L, Ye S, Pang H, Gao GF, Anand K, Bartlam M, Hilgenfeld R, Rao Z ( 2003) The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor. Proc Natl Acad Sci USA 100: 13190–13195.
  • 7
    Yang H, Xie W, Xue X, Yang K, Ma J, Liang W, Zhao Q, Zhou Z, Pei D, Ziebuhr J, Hilgenfeld R, Yuen KY, Wong L, Gao G, Chen S, Chen Z, Ma D, Bartlam M, Rao Z ( 2005) Design of wide-spectrum inhibitors targeting coronavirus main proteases. PLoS Biol 3: e324.
  • 8
    Anand K, Palm GJ, Mesters JR, Siddell SG, Ziebuhr J, Hilgenfeld R ( 2002) Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain. EMBO J 21: 3213–3224.
  • 9
    Graziano V, McGrath WJ, Yang L, Mangel WF ( 2006) SARS CoV main proteinase: the monomer-dimer equilibrium dissociation constant. Biochemistry 45: 14632–14641.
  • 10
    Fan K, Wei P, Feng Q, Chen S, Huang C, Ma L, Lai B, Pei J, Liu Y, Chen J, Lai L ( 2004) Biosynthesis, purification, and substrate specificity of severe acute respiratory syndrome coronavirus 3C-like proteinase. J Biol Chem 279: 1637–1642.
  • 11
    Shi J, Wei Z, Song J ( 2004) Dissection study on the severe acute respiratory syndrome 3C-like protease reveals the critical role of the extra domain in dimerization of the enzyme: defining the extra domain as a new target for design of highly specific protease inhibitors. J Biol Chem 279: 24765–24773.
  • 12
    Zhong N, Zhang S, Zou P, Chen J, Kang X, Li Z, Liang C, Jin C, Xia B ( 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.
  • 13
    Liu Y, Gotte G, Libonati M, Eisenberg D ( 2001) A domain-swapped RNase A dimer with implications for amyloid formation. Nat Struct Biol 8: 211–214.
  • 14
    Bax A ( 1994) Multidimensional nuclear-magnetic-resonance methods for protein studies. Curr Opin Struct Biol 4: 738–744.
  • 15
    Cornilescu G, Delaglio F, Bax A ( 1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13: 289–302.
  • 16
    Wishart DS, Sykes BD, Richards FM ( 1992) The chemical-shift index—a fast and simple method for the assignment of protein secondary structure through NMR-spectroscopy. Biochemistry 31: 1647–1651.
  • 17
    Wishart DS, Sykes BD ( 1994) The C-13 chemical-shift index—a simple method for the identification of protein secondary structure using C-13 chemical-shift data. J Biomol NMR 4: 171–180.
  • 18
    Guntert P, Mumenthaler C, Wuthrich K ( 1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 273: 283–298.
  • 19
    Herrmann T, Guntert P, Wuthrich K ( 2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319: 209–227.
  • 20
    Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ ( 2005) The amber biomolecular simulation programs. J Comput Chem 26: 1668–1688.
    Direct Link:
  • 21
    Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. In: CarterCW,Jr, SweetRM, Eds. ( 1997) Macromolecular crystallography, part A. Academic Press, New York, pp 307–326.
  • 22
    McCoy A, Grosse-Kunstleve R, Adams P, Winn M, Storoni L, Read R ( 2007) Phaser crystallographic software. J Appl Crystallogr 40: 658–674.
    Direct Link:
  • 23
    Emsley P, Cowtan K ( 2004) Coot: model-building tools for molecular graphics. Acta Crystallogr Sect D 60: 2126–2132.
    Direct Link:
  • 24
    Murshudov GN, Vagin AA, Dodson EJ ( 1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr Sect D 53: 240–255.
    Direct Link:
  • 25
    Laskowski R, MacArthur M, Moss D, Thornton J ( 1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26: 283–291.
    Direct Link:
  • 26
    Koradi R, Billeter M, Wuthrich K ( 1996) MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graphics 14: 51–55, 29–32.
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