Dataset Information

Decoding the vital segments in human ATP-dependent RNA helicase.

ABSTRACT: An analysis of the ATP-dependent RNA helicase using known functionally close analogs helps disclose the structural and functional information of the enzyme. The enzyme plays several interlinked biological functions and there is an urgent need to interpret its key active-site residues to infer function and establish role. The human protein q96c10.1 is annotated using tools such as interpro, go and cdd. The physicochemical properties are estimated using the tool protparam. We describe the enzyme protein model developed using modeller to identify active site residues. We used consurf to estimate the structural conservation and is evolutionary relationship is inferred using known close sequence homologs. The active site is predicted using castp and its topological flexibility is estimated through cabs-flex. The protein is annotated as a hydrolase using available data and ddx58 is found as its top-ranked interacting protein partner. We show that about 124 residues are found to be highly conserved among 259 homologs, clustered in 7 clades with the active-site showing low sequence conservation. It is further shown that only 9 loci among the 42 active-site residues are conserved with limited structural fluctuation from the wild type structure. Thus, we document various useful information linked to function, sequence similarity and phylogeny of the enzyme for annotation as potential helicase as designated by uniprot. Data shows limited degree of conserved sequence segments with topological flexibility unlike in other subfamily members of the protein.

SUBMITTER: Kamjula V

PROVIDER: S-EPMC7196165 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Decoding the vital segments in human ATP-dependent RNA helicase.

Kamjula Vandana V Kanneganti Ananya A Metla Rohan R Nidamanuri Kusuma K Idupulapati Sudarshan S Runthala Ashish A

Bioinformation 20200229 2

An analysis of the ATP-dependent RNA helicase using known functionally close analogs helps disclose the structural and functional information of the enzyme. The enzyme plays several interlinked biological functions and there is an urgent need to interpret its key active-site residues to infer function and establish role. The human protein q96c10.1 is annotated using tools such as interpro, go and cdd. The physicochemical properties are estimated using the tool protparam. We describe the enzyme p ...[more]

PMID: 32405168

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Project description:RNA helicases and chaperones are the two major classes of RNA remodeling proteins, which function to remodel RNA structures and/or RNA-protein interactions, and are required for all aspects of RNA metabolism. Although some virus-encoded RNA helicases/chaperones have been predicted or identified, their RNA remodeling activities in vitro and functions in the viral life cycle remain largely elusive. Enteroviruses are a large group of positive-stranded RNA viruses in the Picornaviridae family, which includes numerous important human pathogens. Herein, we report that the nonstructural protein 2CATPase of enterovirus 71 (EV71), which is the major causative pathogen of hand-foot-and-mouth disease and has been regarded as the most important neurotropic enterovirus after poliovirus eradication, functions not only as an RNA helicase that 3'-to-5' unwinds RNA helices in an adenosine triphosphate (ATP)-dependent manner, but also as an RNA chaperone that destabilizes helices bidirectionally and facilitates strand annealing and complex RNA structure formation independently of ATP. We also determined that the helicase activity is based on the EV71 2CATPase middle domain, whereas the C-terminus is indispensable for its RNA chaperoning activity. By promoting RNA template recycling, 2CATPase facilitated EV71 RNA synthesis in vitro; when 2CATPase helicase activity was impaired, EV71 RNA replication and virion production were mostly abolished in cells, indicating that 2CATPase-mediated RNA remodeling plays a critical role in the enteroviral life cycle. Furthermore, the RNA helicase and chaperoning activities of 2CATPase are also conserved in coxsackie A virus 16 (CAV16), another important enterovirus. Altogether, our findings are the first to demonstrate the RNA helicase and chaperoning activities associated with enterovirus 2CATPase, and our study provides both in vitro and cellular evidence for their potential roles during viral RNA replication. These findings increase our understanding of enteroviruses and the two types of RNA remodeling activities.

Dataset Information

Decoding the vital segments in human ATP-dependent RNA helicase.

Publications

Decoding the vital segments in human ATP-dependent RNA helicase.

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