Structure of Sindbis virus core protein reveals a chymotrypsin-like serine proteinase and the organization of the virion

Choi, Hojong; Tong, Liang; Minor, Władek; Dumas, Philippe; Boege, Ulrike; Rossmann, Michael G.; Wengler, Gerd

doi:10.1038/354037a0

Cited by 287 publications

(265 citation statements)

References 62 publications

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“…Similar autoinhibitory structures were observed for the Sindbis virus nucleocapsid protease and the hepatitis C virus NS2 protease (53,54). Inhibition by the unreleased product appears to be a common mechanism underlying the action of cis-only proteases.…”

Section: Discussionsupporting

confidence: 53%

Structure of the Autocatalytic Cysteine Protease Domain of Potyvirus Helper-component Proteinase

Guo

Lin

2011

Journal of Biological Chemistry

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The helper-component proteinase (HC-Pro) of potyvirus is involved in polyprotein processing, aphid transmission, and suppression of antiviral RNA silencing. There is no high resolution structure reported for any part of HC-Pro, hindering mechanistic understanding of its multiple functions. We have determined the crystal structure of the cysteine protease domain of HC-Pro from turnip mosaic virus at 2.0 Å resolution. As a protease, HC-Pro only cleaves a Gly-Gly dipeptide at its own C terminus. The structure represents a postcleavage state in which the cleaved C terminus remains tightly bound at the active site cleft to prevent trans activity. The structure adopts a compact ␣/␤-fold, which differs from papain-like cysteine proteases and shows weak similarity to nsP2 protease from Venezuelan equine encephalitis alphavirus. Nevertheless, the catalytic cysteine and histidine residues constitute an active site that is highly similar to these in papain-like and nsP2 proteases. HC-Pro recognizes a consensus sequence YXVGG around the cleavage site between the two glycine residues. The structure delineates the sequence specificity at sites P1-P4. Structural modeling and covariation analysis across the Potyviridae family suggest a tryptophan residue accounting for the glycine specificity at site P1 . Moreover, a surface of the protease domain is conserved in potyvirus but not in other genera of the Potyviridae family, likely due to extra functional constrain. The structure provides insight into the catalysis mechanism, cis-acting mode, cleavage site specificity, and other functions of the HC-Pro protease domain.

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Section: Discussionsupporting

confidence: 53%

Structure of the Autocatalytic Cysteine Protease Domain of Potyvirus Helper-component Proteinase

Guo

Lin

2011

Journal of Biological Chemistry

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“…The eight-stranded antiparallel virus fold has now been found in many RNA and DNA viral capsids 39 , yet its presence is not entirely universal (for example in the plant RNA tobacco mosaic virus 54,55 , in the RNA phage MS2 56 and in the animal RNA Sindbis virus 57 ). Hence, the eight-stranded antiparallel β-barrel fold is not a prerequisite for assembly of icosahedral structures 58 .…”

Section: Evolutionmentioning

confidence: 99%

Atomic structure of single-stranded DNA bacteriophage ΦX174 and its functional implications

McKenna

Xia

Willingmann

et al. 1992

Nature

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215

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The mechanism of DNA ejection, viral assembly and evolution are related to the structure of bacteriophage ΦX174. The F protein forms a T = 1 capsid whose major folding motif is the eightstranded antiparallel β barrel found in many other icosahedral viruses. Groups of 5 G proteins form 12 dominating spikes that enclose a hydrophilic channel containing some diffuse electron density. Each G protein is a tight β barrel with its strands running radially outwards and with a topology similar to that of the F protein. The 12 'pilot' H proteins per virion may be partially located in the putative ion channel. The small, basic J protein is associated with the DNA and is situated in an interior cleft of the F protein. Tentatively, there are three regions of partially ordered DNA structure, accounting for about 12% of the total genome.Bacteriophage ΦX174 is a small icosahedral virus that contains a single-stranded, closed circular DNA molecule with 5,386 nucleotide bases (for a recent review, see ref. 1). Of the 11 gene products, four (J, F, G and H) participate in the structure of the virion. There are 60 copies each of the J, F and G proteins and 12 copies of the H protein per virion [2][3][4] (Table 1). Electron microscopy of shadowed or negatively stained particles [5][6][7][8] , as well as a threedimensional reconstruction of frozen-hydrated virions (Fig. 1a), clearly show large spikes at the vertices of the icosahedral particles (N.H.O., T.S.B., P.W. and N.L.I., manuscript in preparation). These spikes are about 32 Å long and have a mean diameter of 70 Å. Edgell et al. 3 have shown that these spikes, which can be removed from the capsid with 4 M urea treatment, are composed of G and H proteins. Assuming all 12 spikes are identical, then each spike will contain five G and one H protein 2 . The capsid itself has an external diameter of roughly 260 Å, with a protein shell that is about 30 Å thick, and contains the F and J proteins as well as the single-stranded (ss) DNA. The phage recognizes a lipopolysaccharide (LPS) receptor on the outer cell membrane of Escherichia coli [8][9][10][11] . Host range mutants, which determine which strains of E. coli are infected by ΦX174, map into the F, G and H genes [12][13][14][15] The infectious virion has a relative molecular mass of 6.2 × 10 6 (M r 6,200K) (26% is DNA) 32 . Lysates of infected E. coli contain two components which can be separated by sedimentation through a sucrose gradient 32,33 . The fast band contains the infectious 114S particles whereas the slow band contains noninfectious, 70S particles 32,34,35 . The latter contains about 20% of the normal DNA content with all of the genome represented in the population of particles. Both types of particles can be crystallized into isomorphous monoclinic crystals with space group P2 1 , and cell dimensions a = 305.6, b = 360.8, c = 299.5 Å, β = 92.89° that diffract at least to 2.6-Å resolution 33 . The asymmetric unit of the crystal cell contains one complete particle. We report here the three-dimensional structure...

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“…This region is rich in proline and glycine and contains ∼30 basic residues, suggesting the N-terminus interacts with viral RNA. 33−36 Atomic structures of the CP alone have the Nterminus disordered, 37,38 and in the cryo electron microscopy structure of the virus, the N-terminus is positioned inward, making contacts with the viral RNA. 14,37,39 The C-terminal domain (residues 101−270) is a chymotrypsin-like domain that comprises a majority of the ordered nucleocapsid core seen in the alphavirus structure.…”

Section: ■ Introductionmentioning

confidence: 99%

The Packaging of Different Cargo into Enveloped Viral Nanoparticles

Fan

Tsvetkova²,

Khuong³

et al. 2012

Mol. Pharmaceutics

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Viral nanoparticles used for biomedical applications must be able to discriminate between tumor or virus-infected host cells and healthy host cells. In addition, viral nanoparticles must have the flexibility to incorporate a wide range of cargo, from inorganic metals to mRNAs to small molecules. Alphaviruses are a family of enveloped viruses for which some species are intrinsically capable of systemic tumor targeting. Alphavirus virus-like particles, or viral nanoparticles, can be generated from in vitro self-assembled core-like particles using nonviral nucleic acid. In this work, we expand on the types of cargo that can be incorporated into alphavirus core-like particles and the molecular requirements for packaging this cargo. We demonstrate that different core-like particle templates can be further enveloped to form viral nanoparticles that are capable of cell entry. We propose that alphaviruses can be selectively modified to create viral nanoparticles for biomedical applications and basic research.

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Structure of Sindbis virus core protein reveals a chymotrypsin-like serine proteinase and the organization of the virion

Cited by 287 publications

References 62 publications

Structure of the Autocatalytic Cysteine Protease Domain of Potyvirus Helper-component Proteinase

Structure of the Autocatalytic Cysteine Protease Domain of Potyvirus Helper-component Proteinase

Atomic structure of single-stranded DNA bacteriophage ΦX174 and its functional implications

The Packaging of Different Cargo into Enveloped Viral Nanoparticles

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