A polyadenylylation-specific RNA-contact site on the surface of the bifunctional vaccinia virus RNA modifying protein VP39 that is distinct from the mRNA 5′ end-binding “cleft” 1 1Edited by K. Nagai

Deng, Li; Johnson, Lela; Neveu, John M.; Hardin, Susan H.; Wang, Shimei; Lane, William S.; Gershon, Paul D.

doi:10.1006/jmbi.1998.2417

Cited by 11 publications

(35 citation statements)

References 24 publications

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“…In contrast to VP55, the VP39 subunit has provided high-resolution crystal structures in combination with its methyltransferase cofactor (8), cofactor-product plus methyltransferase substrate RNA fragment (9) and cofactor-product plus intact methyltransferase substrate RNA (10). VP39 appears to possess multiple RNA binding sites (10)(11)(12). Consistent with this, VP39's two RNA end-modifying functions apparently utilize distinct regions of the protein surface (11,12).…”

Section: Introductionmentioning

confidence: 99%

RNA binding characteristics and overall topology of the vaccinia poly(A) polymerase-processivity factor-primer complex

Johnson

Gershon

1999

Nucleic Acids Research

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The vaccinia virus-encoded heterodimer responsible for poly(A) tail elongation comprises a polyadenylylation catalytic subunit (VP55) and associated processivity factor (VP39). We show that monomeric VP39's affinity for RNA homopolymers follows the hierarchy poly(I) >poly(U) >>poly(G) >poly(A) >poly(C), that the heterodimer interacts stably with 40-45 nucleotide nucleic acid segments, and that its homopolymer preference for polyadenylylation priming is comparable to the VP39 affinity hierarchy (above). For oligonucleotide ligands possessing the previously-identified (rU)2-(N)25-rU heterodimer-binding motif, the heterodimer's affinity and base-type preference are mediated via both the (rU)2and rU portions, with the greater contribution coming from (rU)2. VP39's R107 sidechain contributes to specificity at the downstream rU. Substitution of each ribouridylate of the motif with either ribothymidine or 4-thiodeoxythymidine indicated that the downstream rU interacts with both heterodimer subunits, whereas the upstream (rU)2interacts only with VP55. A 'crosslinking SELEX' approach indicated VP39-base proximity around position -10 of a 4-thioribouridine/deoxycytidine ligand pool. Upon incubating the heterodimer with a panel of identical-sequence oligonucleotides derivatized with azidophenacyl bromide at various phosphate positions, those derivatized at positions -11 to -21 photocrosslinked to both subunits in a coordinated manner. This region may therefore pass through a 'cleft' or enclosed 'channel' at the subunit interface.

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Section: Introductionmentioning

confidence: 99%

RNA binding characteristics and overall topology of the vaccinia poly(A) polymerase-processivity factor-primer complex

Johnson

Gershon

1999

Nucleic Acids Research

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“…VP55 acquires processivity by binding VP39 at a dimerization surface region distal to the VP39 methyltransferase cleft [61]. Conformational changes from this interaction occur in the VP39 methyltransferase, and VP55-VP39 interaction has been shown to positionally alter the VP55 RNA contact site [62]. …”

Section: Resultsmentioning

confidence: 99%

Comparative whole genome sequence analysis of wild-type and cidofovir-resistant monkeypoxvirus

Farlow

Ichou

Huggins

et al. 2010

Virol J

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We performed whole genome sequencing of a cidofovir {[(S)-1-(3-hydroxy-2-phosphonylmethoxy-propyl) cytosine] [HPMPC]}-resistant (CDV-R) strain of Monkeypoxvirus (MPV). Whole-genome comparison with the wild-type (WT) strain revealed 55 single-nucleotide polymorphisms (SNPs) and one tandem-repeat contraction. Over one-third of all identified SNPs were located within genes comprising the poxvirus replication complex, including the DNA polymerase, RNA polymerase, mRNA capping methyltransferase, DNA processivity factor, and poly-A polymerase. Four polymorphic sites were found within the DNA polymerase gene. DNA polymerase mutations observed at positions 314 and 684 in MPV were consistent with CDV-R loci previously identified in Vaccinia virus (VACV). These data suggest the mechanism of CDV resistance may be highly conserved across Orthopoxvirus (OPV) species. SNPs were also identified within virulence genes such as the A-type inclusion protein, serine protease inhibitor-like protein SPI-3, Schlafen ATPase and thymidylate kinase, among others. Aberrant chain extension induced by CDV may lead to diverse alterations in gene expression and viral replication that may result in both adaptive and attenuating mutations. Defining the potential contribution of substitutions in the replication complex and RNA processing machinery reported here may yield further insight into CDV resistance and may augment current therapeutic development strategies.

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“…Despite similarities in the N-terminal domain, the VP55 monomer and the VP55-VP39 heterodimer differ profoundly in their primer-binding properties. Notably, the optimal distance between the proximal U and distal UU of the primer is 10 nt greater in the heterodimer than in the VP55 monomer Deng et al, 1999). Since the maximum 'rocking' distance in VP55 is 6.5 Å (above), a distance that is inadequate to absorb 10 nt of additional ssNA, a more likely mechanism for absorption of the longer primer would seem to be primer re-routing in the heterodimer.…”

Section: Figurementioning

confidence: 97%

Domain-level rocking motion within a polymerase that translocates on single-stranded nucleic acid

Zhou

et al. 2013

Acta Crystallogr D Biol Cryst

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Vaccinia virus poly(A) polymerase (VP55) is the only known polymerase that can translocate independently with respect to single‐stranded nucleic acid (ssNA). Previously, its structure has only been solved in the context of the VP39 processivity factor. Here, a crystal structure of unliganded monomeric VP55 has been solved to 2.86 Å resolution, showing the first backbone structural isoforms among either VP55 or its processivity factor (VP39). Backbone differences between the two molecules of VP55 in the asymmetric unit indicated that unliganded monomeric VP55 can undergo a `rocking' motion of the N‐terminal domain with respect to the other two domains, which may be `rigidified' upon VP39 docking. This observation is consistent with previously demonstrated experimental molecular dynamics of the monomer during translocation with respect to nucleic acid and with different mechanisms of translocation in the presence and absence of processivity factor VP39. Side‐chain conformational changes in the absence of ligand were observed at a key primer contact site and at the catalytic center of VP55. The current structure completes the trio of possible structural forms for VP55 and VP39, namely the VP39 monomer, the VP39–VP55 heterodimer and the VP55 monomer.

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A polyadenylylation-specific RNA-contact site on the surface of the bifunctional vaccinia virus RNA modifying protein VP39 that is distinct from the mRNA 5′ end-binding “cleft” 1 1Edited by K. Nagai

Cited by 11 publications

References 24 publications

RNA binding characteristics and overall topology of the vaccinia poly(A) polymerase-processivity factor-primer complex

RNA binding characteristics and overall topology of the vaccinia poly(A) polymerase-processivity factor-primer complex

Comparative whole genome sequence analysis of wild-type and cidofovir-resistant monkeypoxvirus

Domain-level rocking motion within a polymerase that translocates on single-stranded nucleic acid

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