Crystal Structure and Functional Analysis of the SARS-Coronavirus RNA Cap 2′-O-Methyltransferase nsp10/nsp16 Complex
Cellular and viral S-adenosylmethionine-dependent methyltransferases are involved in many regulated processes such as metabolism, detoxification, signal transduction, chromatin remodeling, nucleic acid processing, and mRNA capping. The Severe Acute Respiratory Syndrome coronavirus nsp16 protein is a S-adenosylmethionine-dependent (nucleoside-2′-O)-methyltransferase only active in the presence of its activating partner nsp10. We report the nsp10/nsp16 complex structure at 2.0 Å resolution, which shows nsp10 bound to nsp16 through a ∼930 Å2 surface area in nsp10. Functional assays identify key residues involved in nsp10/nsp16 association, and in RNA binding or catalysis, the latter likely through a SN2-like mechanism. We present two other crystal structures, the inhibitor Sinefungin bound in the S-adenosylmethionine binding pocket and the tighter complex nsp10(Y96F)/nsp16, providing the first structural insight into the regulation of RNA capping enzymes in (+)RNA viruses.
Vyšlo v časopise:
Crystal Structure and Functional Analysis of the SARS-Coronavirus RNA Cap 2′-O-Methyltransferase nsp10/nsp16 Complex. PLoS Pathog 7(5): e32767. doi:10.1371/journal.ppat.1002059
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.ppat.1002059
Souhrn
Cellular and viral S-adenosylmethionine-dependent methyltransferases are involved in many regulated processes such as metabolism, detoxification, signal transduction, chromatin remodeling, nucleic acid processing, and mRNA capping. The Severe Acute Respiratory Syndrome coronavirus nsp16 protein is a S-adenosylmethionine-dependent (nucleoside-2′-O)-methyltransferase only active in the presence of its activating partner nsp10. We report the nsp10/nsp16 complex structure at 2.0 Å resolution, which shows nsp10 bound to nsp16 through a ∼930 Å2 surface area in nsp10. Functional assays identify key residues involved in nsp10/nsp16 association, and in RNA binding or catalysis, the latter likely through a SN2-like mechanism. We present two other crystal structures, the inhibitor Sinefungin bound in the S-adenosylmethionine binding pocket and the tighter complex nsp10(Y96F)/nsp16, providing the first structural insight into the regulation of RNA capping enzymes in (+)RNA viruses.
Zdroje
1. GuMLimaCD 2005 Processing the message: structural insights into capping and decapping mRNA. Curr Opin Struct Biol 15 99 106
2. ShumanS 2001 Structure, mechanism, and evolution of the mRNA capping apparatus. Prog Nucleic Acid Res Mol Biol 66 1 40
3. ShumanS 2002 What messenger RNA capping tells us about eukaryotic evolution. Nat Rev Mol Cell Biol 3 619 625
4. YoneyamaMFujitaT 2010 Recognition of viral nucleic acids in innate immunity. Rev Med Virol 20 4 22
5. ShumanS 2001 The mRNA capping apparatus as drug target and guide to eukaryotic phylogeny. Cold Spring Harb Symp Quant Biol 66 301 312
6. AholaTKaariainenL 1995 Reaction in alphavirus mRNA capping: formation of a covalent complex of nonstructural protein nsP1 with 7-methyl-GMP. Proc Natl Acad Sci U S A 92 507 511
7. OginoTBanerjeeAK 2007 Unconventional mechanism of mRNA capping by the RNA-dependent RNA polymerase of vesicular stomatitis virus. Mol Cell 25 85 97
8. PlotchSJBouloyMUlmanenIKrugRM 1981 A unique cap(m7GpppXm)-dependent influenza virion endonuclease cleaves capped RNAs to generate the primers that initiate viral RNA transcription. Cell 23 847 858
9. RotaPAObersteMSMonroeSSNixWACampagnoliR 2003 Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 300 1394 1399
10. GorbalenyaAEEnjuanesLZiebuhrJSnijderEJ 2006 Nidovirales: evolving the largest RNA virus genome. Virus Res 117 17 37
11. LaiMMPattonCDStohlmanSA 1982 Further characterization of mRNA's of mouse hepatitis virus: presence of common 5′-end nucleotides. J Virol 41 557 565
12. LaiMMStohlmanSA 1981 Comparative analysis of RNA genomes of mouse hepatitis viruses. J Virol 38 661 670
13. van VlietALSmitsSLRottierPJde GrootRJ 2002 Discontinuous and non-discontinuous subgenomic RNA transcription in a nidovirus. EMBO J 21 6571 6580
14. DecrolyEImbertICoutardBBouvetMSeliskoB 2008 Coronavirus nonstructural protein 16 is a cap-0 binding enzyme possessing (nucleoside-2′O)-methyltransferase activity. J Virol 82 8071 8084
15. ChenYCaiHPanJXiangNTienP 2009 Functional screen reveals SARS coronavirus nonstructural protein nsp14 as a novel cap N7-methyltransferase. Proc Natl Acad Sci U S A 106 3484 3489
16. BouvetMDebarnotCImbertISeliskoBSnijderEJ 2010 In vitro reconstitution of SARS-coronavirus mRNA cap methylation. PLoS Pathog 6 e1000863
17. ImbertISnijderEJDimitrovaMGuillemotJC 2008 The SARS-Coronavirus PLnc domain of nsp3 as a replication/transcription scaffolding protein. Virus Res 133 136 148
18. LugariABetziSDecrolyEBonnaudEHermantA 2010 Molecular mapping of the RNA Cap 2′-O-methyltransferase activation interface between SARS coronavirus nsp10 and nsp16. J Biol Chem 285 33230 33241
19. PanJPengXGaoYLiZLuX 2008 Genome-wide analysis of protein-protein interactions and involvement of viral proteins in SARS-CoV replication. PLoS One 3 e3299
20. JosephJSSaikatenduKSSubramanianVNeumanBWBroounA 2006 Crystal structure of nonstructural protein 10 from the severe acute respiratory syndrome coronavirus reveals a novel fold with two zinc-binding motifs. J Virol 80 7894 7901
21. SuDLouZSunFZhaiYYangH 2006 Dodecamer structure of severe acute respiratory syndrome coronavirus nonstructural protein nsp10. J Virol 80 7902 7908
22. SawickiSGSawickiDLYounkerDMeyerYThielV 2005 Functional and genetic analysis of coronavirus replicase-transcriptase proteins. PLoS Pathog 1 e39
23. DonaldsonEFSimsACGrahamRLDenisonMRBaricRS 2007 Murine hepatitis virus replicase protein nsp10 is a critical regulator of viral RNA synthesis. J Virol 81 6356 6368
24. DonaldsonEFGrahamRLSimsACDenisonMRBaricRS 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
25. MartinJLMcMillanFM 2002 SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase fold. Curr Opin Struct Biol 12 783 793
26. VidgrenJSvenssonLALiljasA 1994 Crystal structure of catechol O-methyltransferase. Nature 368 354 358
27. HodelAEGershonPDShiXQuiochoFA 1996 The 1.85 A structure of vaccinia protein VP39: a bifunctional enzyme that participates in the modification of both mRNA ends. Cell 85 247 256
28. De la PenaMKyrieleisOJCusackS 2007 Structural insights into the mechanism and evolution of the vaccinia virus mRNA cap N7 methyl-transferase. EMBO J 26 4913 4925
29. ReinischKMNibertMLHarrisonSC 2000 Structure of the reovirus core at 3.6 A resolution. Nature 404 960 967
30. SuttonGGrimesJMStuartDIRoyP 2007 Bluetongue virus VP4 is an RNA-capping assembly line. Nat Struct Mol Biol 14 449 451
31. EgloffMPBenarrochDSeliskoBRometteJLCanardB 2002 An RNA cap (nucleoside-2′-O-)-methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization. EMBO J 21 2757 2768
32. EgloffMPDecrolyEMaletHSeliskoBBenarrochD 2007 Structural and functional analysis of methylation and 5′-RNA sequence requirements of short capped RNAs by the methyltransferase domain of dengue virus NS5. J Mol Biol 372 723 736
33. RayDShahATilgnerMGuoYZhaoY 2006 West Nile virus 5′-cap structure is formed by sequential guanine N-7 and ribose 2′-O methylations by nonstructural protein 5. J Virol 80 8362 8370
34. BollatiMAlvarezKAssenbergRBarontiCCanardB 2010 Structure and functionality in flavivirus NS-proteins: perspectives for drug design. Antiviral Res 87 125 148
35. SnijderEJBredenbeekPJDobbeJCThielVZiebuhrJ 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
36. BalzariniJDe ClercqESerafinowskiPDorlandEHarrapKR 1992 Synthesis and antiviral activity of some new S-adenosyl-L-homocysteine derivatives. J Med Chem 35 4576 4583
37. DongHZhangBShiPY 2008 Flavivirus methyltransferase: a novel antiviral target. Antiviral Res 80 1 10
38. PughCSBorchardtRTStoneHO 1977 Inhibition of Newcastle disease virion messenger RNA (guanine-7-)-methyltransferase by analogues of S-adenosylhomocysteine. Biochemistry 16 3928 3932
39. PughCSBorchardtRTStoneHO 1978 Sinefungin, a potent inhibitor of virion mRNA(guanine-7-)-methyltransferase, mRNA(nucleoside-2′-)-methyltransferase, and viral multiplication. J Biol Chem 253 4075 4077
40. DebarnotCImbertIFerronFGluaisLVarletI 2011 Crystallization and diffraction analysis of the SARS coronavirus nsp10/nsp16 complex. Acta Crystallogr Sect F Struct Biol Cryst Commun 67 404 8
41. HolmLParkJ 2000 DaliLite workbench for protein structure comparison. Bioinformatics 16 566 567
42. DudevTLimC 2003 Principles governing Mg, Ca, and Zn binding and selectivity in proteins. Chem Rev 103 773 788
43. MarcotrigianoJGingrasACSonenbergNBurleySK 1997 Cocrystal structure of the messenger RNA 5′ cap-binding protein (eIF4E) bound to 7-methyl-GDP. Cell 89 951 961
44. MazzaCSegrefAMattajIWCusackS 2002 Large-scale induced fit recognition of an m(7)GpppG cap analogue by the human nuclear cap-binding complex. EMBO J 21 5548 5557
45. GuilligayDTarendeauFResa-InfantePColomaRCrepinT 2008 The structural basis for cap binding by influenza virus polymerase subunit PB2. Nat Struct Mol Biol 15 500 506
46. QuiochoFAHuGGershonPD 2000 Structural basis of mRNA cap recognition by proteins. Curr Opin Struct Biol 10 78 86
47. HodelAEGershonPDQuiochoFA 1998 Structural basis for sequence-nonspecific recognition of 5′-capped mRNA by a cap-modifying enzyme. Mol Cell 1 443 447
48. LiCXiaYGaoXGershonPD 2004 Mechanism of RNA 2′-O-methylation: evidence that the catalytic lysine acts to steer rather than deprotonate the target nucleophile. Biochemistry 43 5680 5687
49. SigelRKSigelH 2010 A stability concept for metal ion coordination to single-stranded nucleic acids and affinities of individual sites. Acc Chem Res 43 974 984
50. DeySPalAChakrabartiPJaninJ 2010 The subunit interfaces of weakly associated homodimeric proteins. J Mol Biol 398 146 160
51. YoneyamaMKikuchiMNatsukawaTShinobuNImaizumiT 2004 The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses. Nat Immunol 5 730 737
52. MaletHEgloffMPSeliskoBButcherREWrightPJ 2007 Crystal structure of the RNA polymerase domain of the West Nile virus non-structural protein 5. J Biol Chem 282 10678 10689
53. DongHLiuLZouGZhaoYLiZ 2010 Structural and functional analyses of a conserved hydrophobic pocket of flavivirus methyltransferase. J Biol Chem 285 32586 32595
54. McCoyAJGrosse-KunstleveRWAdamsPDWinnMDStoroniLC 2007 Phaser crystallographic software. Journal of applied crystallography 40 658 674
55. CowtanK 2010 Recent developments in classical density modification. Acta Crystallogr D Biol Crystallogr 66 470 478
56. CowtanK 2006 The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr D Biol Crystallogr 62 1002 1011
57. CohenSXMorrisRJFernandezFJBen JelloulMKakarisM 2004 Towards complete validated models in the next generation of ARP/wARP. Acta Crystallogr D Biol Crystallogr 60 2222 2229
58. EmsleyPCowtanK 2004 Coot: model-building tools for molecular graphics. Acta crystallographica Section D, Biological crystallography 60 2126 2132
59. Collaborative Computational Project N 1994 The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50 760 763
60. SaffEBKuijlaarsABJ 1997 Distributing Many Points on a Sphere. Math Intell 19 5 11
61. PeyraneFSeliskoBDecrolyEVasseurJJBenarrochD 2007 High-yield production of short GpppA- and 7MeGpppA-capped RNAs and HPLC-monitoring of methyltransfer reactions at the guanine-N7 and adenosine-2′O positions. Nucleic Acids Res 35 e26
Štítky
Hygiena a epidemiológia Infekčné lekárstvo LaboratóriumČlánok vyšiel v časopise
PLOS Pathogens
2011 Číslo 5
- Očkování proti virové hemoragické horečce Ebola experimentální vakcínou rVSVDG-ZEBOV-GP
- Parazitičtí červi v terapii Crohnovy choroby a dalších zánětlivých autoimunitních onemocnění
- Koronavirus hýbe světem: Víte jak se chránit a jak postupovat v případě podezření?
Najčítanejšie v tomto čísle
- Crystal Structure and Functional Analysis of the SARS-Coronavirus RNA Cap 2′-O-Methyltransferase nsp10/nsp16 Complex
- The OXI1 Kinase Pathway Mediates -Induced Growth Promotion in Arabidopsis
- The Hexamer Structure of the Rift Valley Fever Virus Nucleoprotein Suggests a Mechanism for its Assembly into Ribonucleoprotein Complexes
- Acquisition of Human-Type Receptor Binding Specificity by New H5N1 Influenza Virus Sublineages during Their Emergence in Birds in Egypt