Structure of Foot-and-Mouth Disease Virus RNA-dependent RNA Polymerase and Its Complex with a Template-Primer RNA

Ferrer-Orta, Cristina; Arias, Armando; Pérez-Luque, R.; Escarmı́s, Cristina; Domingo, Esteban; Verdaguer, N.

doi:10.1074/jbc.m405465200

Cited by 203 publications

(364 citation statements)

References 48 publications

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“…1B). The EV71 RdRp (3D pol ) generally shares structure/sequence similarity with homologous RdRps from poliovirus (Thompson and Peersen, 2004), coxsackievirus (Campagnola et al, 2008) rhinovirus (Love et al, 2004) and FMDV (Ferrer-Orta et al, 2004) polymerases in Picornaviridae family. The EV71 RdRp (3D pol ) has six four-amino-acid sequence conserved motifs, which are termed motif A, B, C, D, E and F respectively.…”

Section: Resultsmentioning

confidence: 99%

“…Two features enable us to build a feasible model using the EV71 RdRp apoenzyme structure: the direction of polymerase translocation along the template strand is consistent among the known polymerase structures; and the nascent nucleic acid duplex is known to adopt an approximate A-form conformation in the immediate vicinity of the active site (Jacobo-Molina et al, 1993;Doublie et al, 1998;Huang et al, 1998;Li et al, 1998;Lesburg et al, 1999). We therefore modeled the structure of EV71 RdRp (3D pol ) in complex with the template:primer (5'-CAUGGGCC-3'/5'-GGCCC-3') by superimposing the palm domain with the structure of the FMDV 3D polymerase in complex with the template:primer RNA (PDB code: 1WNE ) (Ferrer-Orta et al, 2004) (Fig. 4).…”

Section: Model Of Ev71 Rdrp (3d Pol ) Complex With Template: Primermentioning

confidence: 99%

“…To date, representative RdRps from five families of RNA viruses have known three-dimensional structures: (1) Picornaviridae, poliovirus (Hansen et al, 1997;Thompson and Peersen, 2004;Thompson et al, 2007), human rhinovirus (Love et al, 2004), coxsackievirus (Campagnola et al, 2008), foot-and-mouth-disease virus (FMDV) (Ferrer-Orta et al, 2004); (2) Caliciviridae, rabbit hemorrhagic disease virus (Ng et al, 2002), Norwalk virus (Zamyatkin et al, 2008); (3) Flaviviridae, hepatitis C virus (Bressanelli et al, 1999;Lesburg et al, 1999), bovine viral diarrhea virus (Choi et al, 2006), Dengue virus (Yap et al, 2007), West Nile virus ; (4) Cystoviridae: phage f6 (Butcher et al, 2001;Salgado et al, 2004); and (5) Reoviridae, reovirus (Tao et al, 2002). The RdRp enzymes share a similar overall structure Figure 1.…”

Section: Introductionmentioning

confidence: 99%

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Structures of EV71 RNA-dependent RNA polymerase in complex with substrate and analogue provide a drug target against the hand-foot-and-mouth disease pandemic in China

Lou

Miao

et al. 2010

Protein Cell

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Enterovirus 71 (EV71), one of the major causative agents for hand-foot-and-mouth disease (HFMD), has caused more than 100 deaths among Chinese children since March 2008. The EV71 genome encodes an RNAdependent RNA polymerase (RdRp), denoted 3D pol , which is central for viral genome replication and is a key target for the discovery of specific antiviral therapeutics. Here we report the crystal structures of EV71 RdRp (3D pol ) and in complex with substrate guanosine-5'-triphosphate and analog 5-bromouridine-5'-triphosphate best to 2.4 Å resolution. The structure of EV71 RdRp (3D pol ) has a wider open thumb domain compared with the most closely related crystal structure of poliovirus RdRp. And the EV71 RdRp (3D pol ) complex with GTP or Br-UTP bounded shows two distinct movements of the polymerase by substrate or analogue binding. The model of the complex with the template:primer derived by superimposition with foot-and-mouth disease virus (FMDV) 3D/RNA complex reveals the likely recognition and binding of template:primer RNA by the polymerase. These results together provide a molecular basis for EV71 RNA replication and reveal a potential target for anti-EV71 drug discovery.

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Section: Resultsmentioning

confidence: 99%

Section: Model Of Ev71 Rdrp (3d Pol ) Complex With Template: Primermentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Structures of EV71 RNA-dependent RNA polymerase in complex with substrate and analogue provide a drug target against the hand-foot-and-mouth disease pandemic in China

Lou

Miao

et al. 2010

Protein Cell

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“…K276 is located at the top of the middle finger and is near the RNA template entry channel, but it does not directly interact with the RNA in any of the picornaviral 3D pol -RNA complexes whose structures have been solved thus far. The structural orientations of the phylogenetically conserved amino acids implicated in the polyadenylation of viral RNA are similar in the atomic structures of 3D pol of enterovirus 71 (35), a group A enterovirus; 3D pol of coxsackievirus B3 (36,37), a group B enterovirus; 3D pol of poliovirus (13,16), a group C enterovirus; 3D pol of rhinovirus type 16 (38,39), species A; 3D pol of rhinovirus type 14 (39), species B; and foot-and-mouth disease virus 3D pol (40,41). These phylogenetically conserved sequences and structures likely contribute to the reiterative transcription of poly(A) and poly(U) sequences during viral RNA replication in these other picornaviruses as well, thereby regulating the lengths of poly(A) at the 3= end of viral RNA.…”

Section: Discussionmentioning

confidence: 96%

Structural Features of a Picornavirus Polymerase Involved in the Polyadenylation of Viral RNA

Kempf

Kelly²,

Springer

et al. 2013

J Virol

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Picornaviruses have 3= polyadenylated RNA genomes, but the mechanisms by which these genomes are polyadenylated during viral replication remain obscure. Based on prior studies, we proposed a model wherein the poliovirus RNA-dependent RNA polymerase (3D pol ) uses a reiterative transcription mechanism while replicating the poly(A) and poly(U) portions of viral RNA templates. To further test this model, we examined whether mutations in 3D pol influenced the polyadenylation of virion RNA. We identified nine alanine substitution mutations in 3D pol that resulted in shorter or longer 3= poly(A) tails in virion RNA. These mutations could disrupt structural features of 3D pol required for the recruitment of a cellular poly(A) polymerase; however, the structural orientation of these residues suggests a direct role of 3D pol in the polyadenylation of RNA genomes. Reaction mixtures containing purified 3D pol and a template RNA with a defined poly(U) sequence provided data consistent with a template-dependent reiterative transcription mechanism for polyadenylation. The phylogenetically conserved structural features of 3D pol involved in the polyadenylation of virion RNA include a thumb domain alpha helix that is positioned in the minor groove of the double-stranded RNA product and lysine and arginine residues that interact with the phosphates of both the RNA template and product strands.P icornaviruses, like many other positive-strand RNA viruses, have RNA genomes with variable-length 3= poly(A) tails (1). The poly(A) tails of picornaviruses are important for viability (2), with the length of the poly(A) tails influencing the magnitudes of both viral mRNA translation and RNA replication (3, 4). RNA sequences and structures within the 3= nontranslated region are reported to influence both the length of poly(A) tails in picornaviral RNA (5) and the efficiency of virus replication (6, 7). Viral RNA-dependent RNA polymerases (3D pol s) are predicted to catalyze the polyadenylation of picornaviral RNA in a template-dependent manner during viral RNA replication (8); however, the mechanisms by which RNA genomes are polyadenylated during viral RNA replication remain obscure. In particular, there is little understanding of the mechanisms regulating the length of poly(A) tails synthesized during RNA replication. The RNA-dependent RNA polymerases of negative-strand RNA viruses reiteratively transcribe a small poly(U) sequence within intergenic regions of the viral RNA genome to produce long poly(A) tails on viral mRNAs (9). In a similar manner, the poliovirus RNA-dependent RNA polymerase can reiteratively transcribe poly(A) and poly(U) sequences during viral RNA replication, producing poly(A) and poly(U) sequences longer than those in the respective template RNAs (8).Viral RNA-dependent RNA polymerases are well studied at the structural level (10-12), yet there have been no reports describing the structural features of viral polymerases involved in the polyadenylation of viral RNA. The RNA-dependent RNA polymerase of picornaviruses a...

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“…The alignment between Ebolavirus RdRP and Bunyavirus RdRP includes both the catalytic domain and a helical bundle connected to its C-terminus. These two domains are conserved among known structures of RdRPs from RNA viruses [84][85][86][87][88] ( Fig. 4A-C).…”

Section: The Zinc-finger Domain Of Vp30mentioning

confidence: 89%

Predictive and comparative analysis of Ebolavirus proteins

2015

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Ebolavirus is the pathogen for Ebola Hemorrhagic Fever (EHF). This disease exhibits a high fatality rate and has recently reached a historically epidemic proportion in West Africa. Out of the 5 known Ebolavirus species, only Reston ebolavirus has lost human pathogenicity, while retaining the ability to cause EHF in long-tailed macaque. Significant efforts have been spent to determine the three-dimensional (3D) structures of Ebolavirus proteins, to study their interaction with host proteins, and to identify the functional motifs in these viral proteins. Here, in light of these experimental results, we apply computational analysis to predict the 3D structures and functional sites for Ebolavirus protein domains with unknown structure, including a zinc-finger domain of VP30, the RNA-dependent RNA polymerase catalytic domain and a methyltransferase domain of protein L. In addition, we compare sequences of proteins that interact with Ebolavirus proteins from RESTV-resistant primates with those from RESTV-susceptible monkeys. The host proteins that interact with GP and VP35 show an elevated level of sequence divergence between the RESTV-resistant and RESTV-susceptible species, suggesting that they may be responsible for host specificity. Meanwhile, we detect variable positions in protein sequences that are likely associated with the loss of human pathogenicity in RESTV, map them onto the 3D structures and compare their positions to known functional sites. VP35 and VP30 are significantly enriched in these potential pathogenicity determinants and the clustering of such positions on the surfaces of VP35 and GP suggests possible uncharacterized interaction sites with host proteins that contribute to the virulence of Ebolavirus.

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Structure of Foot-and-Mouth Disease Virus RNA-dependent RNA Polymerase and Its Complex with a Template-Primer RNA

Cited by 203 publications

References 48 publications

Structures of EV71 RNA-dependent RNA polymerase in complex with substrate and analogue provide a drug target against the hand-foot-and-mouth disease pandemic in China

Structures of EV71 RNA-dependent RNA polymerase in complex with substrate and analogue provide a drug target against the hand-foot-and-mouth disease pandemic in China

Structural Features of a Picornavirus Polymerase Involved in the Polyadenylation of Viral RNA

Predictive and comparative analysis of Ebolavirus proteins

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