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Tracking in atomic detail the functional specializations in viral RecA helicases that occur during evolution.

El Omari K, Meier C, Kainov D, Sutton G, Grimes JM, Poranen MM, Bamford DH, Tuma R, Stuart DI, Mancini EJ - Nucleic Acids Res. (2013)

Bottom Line: We previously dissected the mechanism of RNA translocation for one such phage, 12, and have now investigated three further highly divergent, cystoviral P4 NTPases (from 6, 8 and 13).Although the proteins share a common catalytic core, they have different specificities and control mechanisms, which we map onto divergent N- and C-terminal domains.Thus, the RNA loading and tight coupling of NTPase activity with RNA translocation in 8 P4 is due to a remarkable C-terminal structure, which wraps right around the outside of the molecule to insert into the central hole where RNA binds to coupled L1 and L2 loops, whereas in 12 P4, a C-terminal residue, serine 282, forms a specific hydrogen bond to the N7 of purines ring to confer purine specificity for the 12 enzyme.

View Article: PubMed Central - PubMed

Affiliation: Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK, Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00290 Helsinki, Finland, Department of Environmental Research, Siauliai University, Vilniaus gatvė 88, 76285 Siauliai, Lithuania, Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK, Department of Biosciences, University of Helsinki, Biocenter 2, PO Box 56, 00014 Helsinki, Finland, Institute of Biotechnology, University of Helsinki, Biocenter 2, PO Box 56, 00014 Helsinki, Finland and Astbury Centre for Structural Molecular Biology and School of Cellular and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.

ABSTRACT
Many complex viruses package their genomes into empty protein shells and bacteriophages of the Cystoviridae family provide some of the simplest models for this. The cystoviral hexameric NTPase, P4, uses chemical energy to translocate single-stranded RNA genomic precursors into the procapsid. We previously dissected the mechanism of RNA translocation for one such phage, 12, and have now investigated three further highly divergent, cystoviral P4 NTPases (from 6, 8 and 13). High-resolution crystal structures of the set of P4s allow a structure-based phylogenetic analysis, which reveals that these proteins form a distinct subfamily of the RecA-type ATPases. Although the proteins share a common catalytic core, they have different specificities and control mechanisms, which we map onto divergent N- and C-terminal domains. Thus, the RNA loading and tight coupling of NTPase activity with RNA translocation in 8 P4 is due to a remarkable C-terminal structure, which wraps right around the outside of the molecule to insert into the central hole where RNA binds to coupled L1 and L2 loops, whereas in 12 P4, a C-terminal residue, serine 282, forms a specific hydrogen bond to the N7 of purines ring to confer purine specificity for the 12 enzyme.

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The C-terminal domain of ɸ8 P4. (A) Surface presentation of the ɸ8 P4Δ281 (left) and the full-length protein (right). The C-terminal domain is coloured in red. (B) A model for ssRNA induced displacement of the C-terminal domain in ɸ8 P4 hexamer.
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gkt713-F8: The C-terminal domain of ɸ8 P4. (A) Surface presentation of the ɸ8 P4Δ281 (left) and the full-length protein (right). The C-terminal domain is coloured in red. (B) A model for ssRNA induced displacement of the C-terminal domain in ɸ8 P4 hexamer.

Mentions: Based on transient cooperative exposure of subunit interfaces to HDX on RNA binding (residues 198–209 in Figure 7), it was suggested that RNA enters the central channel via a transient ring opening (37). The deletion of the C-terminal portion of the protein (residues 282–321) more than doubles the diameter of the central channel (from 13 to 30 Å), as the C-terminus wraps upwards from the base of the hexamer, along the inter-subunit cleft, to stick down into the central channel (Figure 8). As the C-terminal domain is (i) necessary for ATP hydrolysis (data not shown), (ii) restricts the diameter of the central channel and (iii) blocks the interface through which RNA is thought to be loaded, we postulate that the C-terminal region needs to be displaced by RNA for ring opening and subsequent ATP hydrolysis to occur. To verify this hypothesis, previous HDX experiments (37) were further analysed by mapped to the ɸ8 P4 structure.Figure 7.


Tracking in atomic detail the functional specializations in viral RecA helicases that occur during evolution.

El Omari K, Meier C, Kainov D, Sutton G, Grimes JM, Poranen MM, Bamford DH, Tuma R, Stuart DI, Mancini EJ - Nucleic Acids Res. (2013)

The C-terminal domain of ɸ8 P4. (A) Surface presentation of the ɸ8 P4Δ281 (left) and the full-length protein (right). The C-terminal domain is coloured in red. (B) A model for ssRNA induced displacement of the C-terminal domain in ɸ8 P4 hexamer.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814363&req=5

gkt713-F8: The C-terminal domain of ɸ8 P4. (A) Surface presentation of the ɸ8 P4Δ281 (left) and the full-length protein (right). The C-terminal domain is coloured in red. (B) A model for ssRNA induced displacement of the C-terminal domain in ɸ8 P4 hexamer.
Mentions: Based on transient cooperative exposure of subunit interfaces to HDX on RNA binding (residues 198–209 in Figure 7), it was suggested that RNA enters the central channel via a transient ring opening (37). The deletion of the C-terminal portion of the protein (residues 282–321) more than doubles the diameter of the central channel (from 13 to 30 Å), as the C-terminus wraps upwards from the base of the hexamer, along the inter-subunit cleft, to stick down into the central channel (Figure 8). As the C-terminal domain is (i) necessary for ATP hydrolysis (data not shown), (ii) restricts the diameter of the central channel and (iii) blocks the interface through which RNA is thought to be loaded, we postulate that the C-terminal region needs to be displaced by RNA for ring opening and subsequent ATP hydrolysis to occur. To verify this hypothesis, previous HDX experiments (37) were further analysed by mapped to the ɸ8 P4 structure.Figure 7.

Bottom Line: We previously dissected the mechanism of RNA translocation for one such phage, 12, and have now investigated three further highly divergent, cystoviral P4 NTPases (from 6, 8 and 13).Although the proteins share a common catalytic core, they have different specificities and control mechanisms, which we map onto divergent N- and C-terminal domains.Thus, the RNA loading and tight coupling of NTPase activity with RNA translocation in 8 P4 is due to a remarkable C-terminal structure, which wraps right around the outside of the molecule to insert into the central hole where RNA binds to coupled L1 and L2 loops, whereas in 12 P4, a C-terminal residue, serine 282, forms a specific hydrogen bond to the N7 of purines ring to confer purine specificity for the 12 enzyme.

View Article: PubMed Central - PubMed

Affiliation: Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK, Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00290 Helsinki, Finland, Department of Environmental Research, Siauliai University, Vilniaus gatvė 88, 76285 Siauliai, Lithuania, Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK, Department of Biosciences, University of Helsinki, Biocenter 2, PO Box 56, 00014 Helsinki, Finland, Institute of Biotechnology, University of Helsinki, Biocenter 2, PO Box 56, 00014 Helsinki, Finland and Astbury Centre for Structural Molecular Biology and School of Cellular and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.

ABSTRACT
Many complex viruses package their genomes into empty protein shells and bacteriophages of the Cystoviridae family provide some of the simplest models for this. The cystoviral hexameric NTPase, P4, uses chemical energy to translocate single-stranded RNA genomic precursors into the procapsid. We previously dissected the mechanism of RNA translocation for one such phage, 12, and have now investigated three further highly divergent, cystoviral P4 NTPases (from 6, 8 and 13). High-resolution crystal structures of the set of P4s allow a structure-based phylogenetic analysis, which reveals that these proteins form a distinct subfamily of the RecA-type ATPases. Although the proteins share a common catalytic core, they have different specificities and control mechanisms, which we map onto divergent N- and C-terminal domains. Thus, the RNA loading and tight coupling of NTPase activity with RNA translocation in 8 P4 is due to a remarkable C-terminal structure, which wraps right around the outside of the molecule to insert into the central hole where RNA binds to coupled L1 and L2 loops, whereas in 12 P4, a C-terminal residue, serine 282, forms a specific hydrogen bond to the N7 of purines ring to confer purine specificity for the 12 enzyme.

Show MeSH
Related in: MedlinePlus