Crystal structure of the C-terminal 2′,5′-phosphodiesterase domain of group a rotavirus protein VP3

Brandmann, Tobias; Jinek, Martin

doi:10.1002/prot.24794

Cited by 15 publications

(15 citation statements)

References 36 publications

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“…1A and 2C). This finding is consistent with a recently reported structure for the VP3 CTD of another simian RVA (strain SA11) (34). The two H⌽(S/ T)⌽ motifs, consisting of H718, L719, T720, and F721 from the ␤2-strand and H797, I798, T799, and L800 from the ␤5-strand, are located adjacent to one another at the base of the catalytic cleft.…”

Section: Resultssupporting

confidence: 92%

“…In the apo VP3 CTD crystal structure, the R loop and R792 exhibit significantly different positioning and side chain orientation than those of apo AKAP7. This is also true for the apo VP3 CTD structure of RVA strain SA11 (34). To engage the base of the 5= adenosine and the phosphate moieties of the second adenosine, this loop changes conformation and moves toward the substrate and catalytic site by several angstroms (Fig.…”

Section: Discussionmentioning

confidence: 73%

See 1 more Smart Citation

Structural Basis for 2′-5′-Oligoadenylate Binding and Enzyme Activity of a Viral RNase L Antagonist

Ogden

Jha

et al. 2015

J Virol

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Synthesis of 2=-5=-oligoadenylates (2-5A) by oligoadenylate synthetase (OAS) is an important innate cellular response that limits viral replication by activating the latent cellular RNase, RNase L, to degrade single-stranded RNA. Some rotaviruses and coronaviruses antagonize the OAS/RNase L pathway through the activity of an encoded 2H phosphoesterase domain that cleaves 2-5A. These viral 2H phosphoesterases are phylogenetically related to the cellular A kinase anchoring protein 7 (AKAP7) and share a core structure and an active site that contains two well-defined H⌽(S/T)⌽ (where ⌽ is a hydrophobic residue) motifs, but their mechanism of substrate binding is unknown. Here, we report the structures of a viral 2H phosphoesterase, the C-terminal domain (CTD) of the group A rotavirus (RVA) VP3 protein, both alone and in complex with 2-5A. The domain forms a compact fold, with a concave ␤-sheet that contains the catalytic cleft, but it lacks two ␣-helical regions and two ␤-strands observed in AKAP7 and other 2H phosphoesterases. The cocrystal structure shows significant conformational changes in the R loop upon ligand binding. Bioinformatics and biochemical analyses reveal that conserved residues and residues required for catalytic activity and substrate binding comprise the catalytic motifs and a region on one side of the binding cleft. We demonstrate that the VP3 CTD of group B rotavirus, but not that of group G, cleaves 2-5A. These findings suggest that the VP3 CTD is a streamlined version of a 2H phosphoesterase with a ligand-binding mechanism that is shared among 2H phosphodiesterases that cleave 2-5A. IMPORTANCEThe C-terminal domain (CTD) of rotavirus VP3 is a 2H phosphoesterase that cleaves 2=-5=-oligoadenylates (2-5A), potent activators of an important innate cellular antiviral pathway. 2H phosphoesterase superfamily proteins contain two conserved catalytic motifs and a proposed core structure. Here, we present structures of a viral 2H phosphoesterase, the rotavirus VP3 CTD, alone and in complex with its substrate, 2-5A. The domain lacks two ␣-helical regions and ␤-strands present in other 2H phosphoesterases. A loop of the protein undergoes significant structural changes upon substrate binding. Together with our bioinformatics and biochemical findings, the crystal structures suggest that the RVA VP3 CTD domain is a streamlined version of a cellular enzyme that shares a ligand-binding mechanism with other 2H phosphodiesterases that cleave 2-5A but differs from those of 2H phosphodiesterases that cleave other substrates. These findings may aid in the future design of antivirals targeting viral phosphodiesterases with cleavage specificity for 2-5A. O ne of the earliest steps in the battle between a virus and its host is the detection of pathogen-associated molecular patterns by cellular sensors. For RNA viruses, these patterns may be found in RNA products synthesized during viral transcription and replication. A number of cytoplasmic cellular molecules have been described that sense foreign RNA and resp...

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Section: Resultssupporting

confidence: 92%

Section: Discussionmentioning

confidence: 73%

Structural Basis for 2′-5′-Oligoadenylate Binding and Enzyme Activity of a Viral RNase L Antagonist

Ogden

Jha

et al. 2015

J Virol

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“…It is a multi-functional capping enzyme of 835 amino acids [65]. While the N-terminal region of~690 residues contains domains needed for mRNA capping functions (a variable N-terminal domain, a guanine-N7-methyltransferase (N7-MTase) domain, a ribose-2 0 -O -methyltransferase domain, a guanylyltransferase and RNA 5 0triphosphatase (GTPase/RTPase) domain), the C-terminal region of~150 amino acids possesses a 2 0 ,5 0 -phosphodiesterase (PDE) activity that cleaves 2 0 -5 0 -oligoadenylate [66,67], thereby preventing RNase L activation [66,67]. Apart from capping-associated activities, VP3 is also associated with virulence.…”

Section: Structural Protein Vp3mentioning

confidence: 99%

“…In its N7-MTase and GTase/RTPase domains, VP3 has some sequence motifs that are conserved among the rotavirus and orbivirus species. The conserved residues in the N7-MTase domain are located in region 134-139, whereas in GTase/RTPase domain, residues from 552 to 555 and Ser527, Arg531, Trp571, His610 are highly conserved [66,67]. Even though this multifunctional protein has a mean PPID score of 0% {Table 1}, individual predictors, such as PONDR Ò VLXT, PONDR Ò VSL2, and PONDR Ò FIT have predicted short stretches of Table 2 MoRF analysis of all proteins of SA11 rotavirus strain by four different tools.…”

Section: Structural Protein Vp3mentioning

confidence: 99%

Understanding the penetrance of intrinsic protein disorder in rotavirus proteome

Kumar

Singh

Kumar

et al. 2020

International Journal of Biological Macromolecules

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a b s t r a c tRotavirus is a major cause of severe acute gastroenteritis in the infants and young children. The past decade has evidenced the role of intrinsically disordered proteins/regions (IDPs)/(IDPRs) in viral and other diseases. In general, (IDPs)/(IDPRs) are considered as dynamic conformational ensembles that devoid of a specific 3D structure, being associated with various important biological phenomena. Viruses utilize IDPs/IDPRs to survive in harsh environments, to evade the host immune system, and to highjack and manipulate host cellular proteins. The role of IDPs/IDPRs in Rotavirus biology and pathogenicity are not assessed so far, therefore, we have designed this study to deeply look at the penetrance of intrinsic disorder in rotavirus proteome consisting 12 proteins encoded by 11 segments of viral genome. Also, for all human rotaviral proteins, we have deciphered molecular recognition features (MoRFs), which are disorder based binding sites in proteins. Our study shows the wide spread of intrinsic disorder in several rotavirus proteins, primarily the nonstructural proteins NSP3, NSP4, and NSP5 that are involved in viral replication, translation, viroplasm formation and/or maturation. This study may serve as a primer for understanding the role of IDPs/MoRFs in rotavirus biology, design of alternative therapeutic strategies, and development of disorder-based drugs.

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“…2a). The structures of AKAP7 CD (PDB ID 2VFY) and VP3-CTD (PDB ID 5AF2), which exhibit substantial structural homology, have previously been determined (Brandmann & Jinek, 2015;Ogden et al, 2015). The structural alignment of ns2 7-167 , AKAP7 CD and VP3-CTD indicated that all of these structures form similar positive electrostatic concave regions in the 29,59-PDE activity domain, which is putatively involved in the binding and cleavage of 2-5A ( Fig.…”

mentioning

confidence: 96%

Crystal structure of the mouse hepatitis virus ns2 phosphodiesterase domain that antagonizes RNase L activation

Sui

Huang

Jha

et al. 2016

Journal of General Virology

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Prior studies have demonstrated that the mouse hepatitis virus (MHV) A59 strain ns2 protein is a member of the 2H phosphoesterase family and exhibits 29,59-phosphodiesterase (PDE) activity. During the IFN antiviral response, ns2 cleaves 29,59-oligoadenylate (2-5A), a key mediator of RNase L activation, thereby subverting the activation of RNase L and evading host innate immunity. However, the mechanism of 2-5A cleavage by ns2 remains unclear. Here, we present the crystal structure of the MHV ns2 PDE domain and demonstrate a PDE fold similar to that of the cellular protein, a kinase anchoring protein 7 central domain (AKAP7 CD ) and rotavirus VP3 carboxy-terminal domain. The structure displays a pair of strictly conserved HxT/Sx motifs and forms a deep, positively charged catalytic groove with b-sheets and an arginine-containing loop. These findings provide insight into the structural basis for 2-5A binding of MHV ns2.

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Crystal structure of the C-terminal 2′,5′-phosphodiesterase domain of group a rotavirus protein VP3

Cited by 15 publications

References 36 publications

Structural Basis for 2′-5′-Oligoadenylate Binding and Enzyme Activity of a Viral RNase L Antagonist

Structural Basis for 2′-5′-Oligoadenylate Binding and Enzyme Activity of a Viral RNase L Antagonist

Understanding the penetrance of intrinsic protein disorder in rotavirus proteome

Crystal structure of the mouse hepatitis virus ns2 phosphodiesterase domain that antagonizes RNase L activation

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