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==Mutant M16A of RNA dependent RNA polymerase 3D from Foot-and-Mouth disease Virus==
<StructureSection load='6gvv' size='340' side='right'caption='[[6gvv]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6gvv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aphthovirus_c Aphthovirus c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GVV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GVV FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6gvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gvv OCA], [http://pdbe.org/6gvv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6gvv RCSB], [http://www.ebi.ac.uk/pdbsum/6gvv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6gvv ProSAT]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/POLG_FMDVS POLG_FMDVS]] The leader protease autocatalytically cleaves itself from the polyprotein at the L/VP0 junction. It cleaves the host translation initiation factors EIF4G1 and EIF4G3, in order to shut down the capped cellular mRNA transcription (By similarity).  Capsid proteins VP1, VP2, VP3 and VP4 form a closed capsid enclosing the viral positive strand RNA genome. VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll. Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes. The capsid interacts with host heparan sulfate and various integrins (alphavbeta1, alphavbeta3, alpha5beta1, alphavbeta6, alphavbeta8) to provide virion attachment to target Attachment via host integrins induces virion internalization predominantly through clathrin-mediated endocytosis (By similarity).  Protein VP0: VP0 precursor is a component of immature procapsids (By similarity).  Protein 2B: Affects membrane integrity and cause an increase in membrane permeability (By similarity).  Protein 2C: Associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity).  Protein 3A, via its hydrophobic domain, serves as membrane anchor (By similarity).  Protein 3B-1, 3B-2 and 3B-3 are covalently linked to the 5'-end of both the positive-strand and negative-strand genomic RNAs. They acts as a genome-linked replication primer (By similarity).  Protease 3C: cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind cooperatively to the protease (By similarity).  RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity). 
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== Publication Abstract from PubMed ==
Viral RNA-dependent RNA polymerases (RdRps) are major determinants of high mutation rates and generation of mutant spectra that mediate RNA virus adaptability. The RdRp of the picornavirus foot-and-mouth disease virus (FMDV), termed 3D, is a multifunctional protein that includes a nuclear localization signal (NLS) in its N-terminal region. Previous studies documented that some amino acid substitutions within the NLS altered nucleotide recognition and enhanced the incorporation of the mutagenic purine analogue ribavirin in viral RNA, but the mutants tested were not viable and their response to lethal mutagenesis could not be studied. Here we demonstrate that NLS amino acid substitution M16A of FMDV serotype C does not affect infectious virus production but accelerates ribavirin-mediated virus extinction. The mutant 3D displays similar polymerase activity, RNA binding, and copying processivity than the wild type enzyme, but increased ribavirin-triphosphate incorporation. Crystal structures of the mutant 3D in the apo and RNA bound forms reveal an expansion of the template entry channel due to the replacement of the bulky Met by Ala. This is a major difference with other 3D mutants with altered nucleotide analogue recognition. Remarkably, two distinct loop beta9-alpha11 conformations distinguish 3Ds that exhibit higher or lower ribavirin incorporation than the wild type enzyme. This difference identifies a specific molecular determinant of ribavirin sensitivity of FMDV. Comparison of several polymerase mutants indicates that different domains of the molecule can modify nucleotide recognition and response to lethal mutagenesis. The connection of this observation with current views on quasispecies adaptability is discussed.IMPORTANCE The nuclear localization signal (NLS) of the foot-and-mouth disease virus (FMDV) polymerase includes residues that modulate the sensitivity to mutagenic agents. Here we have described a viable NLS mutant with an amino acid replacement that facilitates virus extinction by ribavirin. The corresponding polymerase shows increased incorporation of ribavirin-triphosphate, and local structural modifications that implicate the template entry channel. Specifically, comparison of the structure of ribavirin-sensitive and ribavirin-resistant FMDV polymerases has identified loop beta9-alpha11 conformation as determinant of sensitivity to ribavirin mutagenesis.

Contribution of a multifunctional polymerase region of foot-and-mouth disease virus to lethal mutagenesis.,de la Higuera I, Ferrer-Orta C, Moreno E, de Avila AI, Soria ME, Singh K, Caridi F, Sobrino F, Sarafianos SG, Perales C, Verdaguer N, Domingo E J Virol. 2018 Aug 1. pii: JVI.01119-18. doi: 10.1128/JVI.01119-18. PMID:30068642<ref>PMID:30068642</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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==See Also==
*[[RNA polymerase|RNA polymerase]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Aphthovirus c]]
[[Category: Large Structures]]
[[Category: Orta, C Ferrer]]
[[Category: Verdaguer, N]]
[[Category: Closed right hand conformation]]
[[Category: Picornavirus]]
[[Category: Rna dependent rna polymerase]]
[[Category: Viral protein]]