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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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Related in: MedlinePlus

Structure-based phylogenetic tree of ATPase enzymes. The matrix of evolutionary distances was calculated with SHP (56). The rectangle corresponds to a close-up view of the members of the RecA family. Abbreviations (In alphabetical order; Protein Data Bank accession codes are quoted in brackets): AfGspE, archaeal secretion ATPase, (2Oap); CFTR, Cystic Fibrosis Transmembrane Conductance Regulation, (1Xmi); Clamp Loader, eukaryotic clamp loader, (1Sxj); CobA, corrinoid adenosyltransferase, (1G64); CobU, adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase, (1Cbu); DMC1, meiotic recombination protein, (2Zjb); DnaB, Thermus aquaticus DNAb, (2Q6t); Elp4, elongator complex protein 4, (4A8j); ESCN, prototypical T3ss ATPase EscN, (2Obl); F1-ATP Synthase-α, ATP synthase subunit-α heart isoform, (2Jj1); F1-ATPase-β, bovine mitochondrial F1-ATPase, (1E1r); FbpC, Fe(3+) ions import ATP-binding protein FbpC, (3Fvq); FtsK, DNA translocase FtsK, (2Iut); G40P, ATPase domain of G40P, (3Bh0); Get3, ATPase Get3, (3Sja); GkDnaC, Geobacillus kaustophilus DnaC, (2Vyf); GsDnaB, Geobacillus stearothermophilus DnaB, (2R6c); IoID, Aquifex Aeolicus ABC transporter, (2Pcj); KaiC, Circadian clock protein kinase KaiC, (3K0e); MalK, maltose/maltodextrin import ATP-binding protein, (2Awn); MipZ, bacterial cell division regulator protein MipZ, (2Xit); MMAA, methylmalonic aciduria type A protein, (2Www); Msb8, Thermotoga maritima Abc transporter ATPp-binding protein, (1Vpl); MutS, DNA mismatch repair protein MutS, (1Ewq); P-gp, multidrug resistance protein Pgp-1, (4F4c); PH0284, Upf0273 Protein Ph0284, (2Dr3); PilT, twitching motility protein PilT, (2Gsz); Psy3, Platinum sensitivity protein 3, (4Dt1); Rad50, Dna Double-Strand Break Repair Rad50 Atpase, (3Qku); Rad51, DNA repair protein Rad51, (1Szp); RadA, DNA repair and recombination protein RadA, (4Dc9); RecA, Recombinase A, (1Mo4); RepA, regulatory protein RepA, (1G8y); Rho, transcription termination factor Rho, (3Ice); Rli1p, translation initiation factor, (3J16); RNT1, regulator of nonsense transcripts 1, (2Wjy); SMC, chromosome partition protein, (4I99); Sso2452, putative uncharacterized protein, (2W0m); T7Gp4, T7 DNA Primase/Helicase, (1Cr1); TK, thymidine kinase, (2Ja1); TrwB, conjugal transfer protein TrwB, (1E9r); V1-ATPase, V-Type sodium ATPase, (3VR4); VirB4, type IV secretory pathway Virb4 components-like protein, (4Ag6); Vps4, vacuolar protein sorting-associated protein 4, (3Eih); XDP, Xpd/Rad3 related DNA helicase, (3Crv).
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gkt713-F4: Structure-based phylogenetic tree of ATPase enzymes. The matrix of evolutionary distances was calculated with SHP (56). The rectangle corresponds to a close-up view of the members of the RecA family. Abbreviations (In alphabetical order; Protein Data Bank accession codes are quoted in brackets): AfGspE, archaeal secretion ATPase, (2Oap); CFTR, Cystic Fibrosis Transmembrane Conductance Regulation, (1Xmi); Clamp Loader, eukaryotic clamp loader, (1Sxj); CobA, corrinoid adenosyltransferase, (1G64); CobU, adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase, (1Cbu); DMC1, meiotic recombination protein, (2Zjb); DnaB, Thermus aquaticus DNAb, (2Q6t); Elp4, elongator complex protein 4, (4A8j); ESCN, prototypical T3ss ATPase EscN, (2Obl); F1-ATP Synthase-α, ATP synthase subunit-α heart isoform, (2Jj1); F1-ATPase-β, bovine mitochondrial F1-ATPase, (1E1r); FbpC, Fe(3+) ions import ATP-binding protein FbpC, (3Fvq); FtsK, DNA translocase FtsK, (2Iut); G40P, ATPase domain of G40P, (3Bh0); Get3, ATPase Get3, (3Sja); GkDnaC, Geobacillus kaustophilus DnaC, (2Vyf); GsDnaB, Geobacillus stearothermophilus DnaB, (2R6c); IoID, Aquifex Aeolicus ABC transporter, (2Pcj); KaiC, Circadian clock protein kinase KaiC, (3K0e); MalK, maltose/maltodextrin import ATP-binding protein, (2Awn); MipZ, bacterial cell division regulator protein MipZ, (2Xit); MMAA, methylmalonic aciduria type A protein, (2Www); Msb8, Thermotoga maritima Abc transporter ATPp-binding protein, (1Vpl); MutS, DNA mismatch repair protein MutS, (1Ewq); P-gp, multidrug resistance protein Pgp-1, (4F4c); PH0284, Upf0273 Protein Ph0284, (2Dr3); PilT, twitching motility protein PilT, (2Gsz); Psy3, Platinum sensitivity protein 3, (4Dt1); Rad50, Dna Double-Strand Break Repair Rad50 Atpase, (3Qku); Rad51, DNA repair protein Rad51, (1Szp); RadA, DNA repair and recombination protein RadA, (4Dc9); RecA, Recombinase A, (1Mo4); RepA, regulatory protein RepA, (1G8y); Rho, transcription termination factor Rho, (3Ice); Rli1p, translation initiation factor, (3J16); RNT1, regulator of nonsense transcripts 1, (2Wjy); SMC, chromosome partition protein, (4I99); Sso2452, putative uncharacterized protein, (2W0m); T7Gp4, T7 DNA Primase/Helicase, (1Cr1); TK, thymidine kinase, (2Ja1); TrwB, conjugal transfer protein TrwB, (1E9r); V1-ATPase, V-Type sodium ATPase, (3VR4); VirB4, type IV secretory pathway Virb4 components-like protein, (4Ag6); Vps4, vacuolar protein sorting-associated protein 4, (3Eih); XDP, Xpd/Rad3 related DNA helicase, (3Crv).

Mentions: Structural classification based on the ATPase core domain shows that cystovirus P4 proteins are closely related to each other and only distantly related to other P-loop ATPases (Figure 4 and Supplementary Figure S2). They most closely resemble RecA-type ATPases (35), such as ATP synthase-like proteins (RHO, F1-ATPase, etc.), RecA-like proteins (RepA, T7 gp4, etc.) and Rad51-like protein (Rad51, RecA, etc.). Many of these proteins are involved in nucleotide repair and recombination and have similar functional properties to P4 proteins. This indicates that the cystoviral P4 proteins form a distinct subfamily of RecA-type ATPases.Figure 4.


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)

Structure-based phylogenetic tree of ATPase enzymes. The matrix of evolutionary distances was calculated with SHP (56). The rectangle corresponds to a close-up view of the members of the RecA family. Abbreviations (In alphabetical order; Protein Data Bank accession codes are quoted in brackets): AfGspE, archaeal secretion ATPase, (2Oap); CFTR, Cystic Fibrosis Transmembrane Conductance Regulation, (1Xmi); Clamp Loader, eukaryotic clamp loader, (1Sxj); CobA, corrinoid adenosyltransferase, (1G64); CobU, adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase, (1Cbu); DMC1, meiotic recombination protein, (2Zjb); DnaB, Thermus aquaticus DNAb, (2Q6t); Elp4, elongator complex protein 4, (4A8j); ESCN, prototypical T3ss ATPase EscN, (2Obl); F1-ATP Synthase-α, ATP synthase subunit-α heart isoform, (2Jj1); F1-ATPase-β, bovine mitochondrial F1-ATPase, (1E1r); FbpC, Fe(3+) ions import ATP-binding protein FbpC, (3Fvq); FtsK, DNA translocase FtsK, (2Iut); G40P, ATPase domain of G40P, (3Bh0); Get3, ATPase Get3, (3Sja); GkDnaC, Geobacillus kaustophilus DnaC, (2Vyf); GsDnaB, Geobacillus stearothermophilus DnaB, (2R6c); IoID, Aquifex Aeolicus ABC transporter, (2Pcj); KaiC, Circadian clock protein kinase KaiC, (3K0e); MalK, maltose/maltodextrin import ATP-binding protein, (2Awn); MipZ, bacterial cell division regulator protein MipZ, (2Xit); MMAA, methylmalonic aciduria type A protein, (2Www); Msb8, Thermotoga maritima Abc transporter ATPp-binding protein, (1Vpl); MutS, DNA mismatch repair protein MutS, (1Ewq); P-gp, multidrug resistance protein Pgp-1, (4F4c); PH0284, Upf0273 Protein Ph0284, (2Dr3); PilT, twitching motility protein PilT, (2Gsz); Psy3, Platinum sensitivity protein 3, (4Dt1); Rad50, Dna Double-Strand Break Repair Rad50 Atpase, (3Qku); Rad51, DNA repair protein Rad51, (1Szp); RadA, DNA repair and recombination protein RadA, (4Dc9); RecA, Recombinase A, (1Mo4); RepA, regulatory protein RepA, (1G8y); Rho, transcription termination factor Rho, (3Ice); Rli1p, translation initiation factor, (3J16); RNT1, regulator of nonsense transcripts 1, (2Wjy); SMC, chromosome partition protein, (4I99); Sso2452, putative uncharacterized protein, (2W0m); T7Gp4, T7 DNA Primase/Helicase, (1Cr1); TK, thymidine kinase, (2Ja1); TrwB, conjugal transfer protein TrwB, (1E9r); V1-ATPase, V-Type sodium ATPase, (3VR4); VirB4, type IV secretory pathway Virb4 components-like protein, (4Ag6); Vps4, vacuolar protein sorting-associated protein 4, (3Eih); XDP, Xpd/Rad3 related DNA helicase, (3Crv).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gkt713-F4: Structure-based phylogenetic tree of ATPase enzymes. The matrix of evolutionary distances was calculated with SHP (56). The rectangle corresponds to a close-up view of the members of the RecA family. Abbreviations (In alphabetical order; Protein Data Bank accession codes are quoted in brackets): AfGspE, archaeal secretion ATPase, (2Oap); CFTR, Cystic Fibrosis Transmembrane Conductance Regulation, (1Xmi); Clamp Loader, eukaryotic clamp loader, (1Sxj); CobA, corrinoid adenosyltransferase, (1G64); CobU, adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase, (1Cbu); DMC1, meiotic recombination protein, (2Zjb); DnaB, Thermus aquaticus DNAb, (2Q6t); Elp4, elongator complex protein 4, (4A8j); ESCN, prototypical T3ss ATPase EscN, (2Obl); F1-ATP Synthase-α, ATP synthase subunit-α heart isoform, (2Jj1); F1-ATPase-β, bovine mitochondrial F1-ATPase, (1E1r); FbpC, Fe(3+) ions import ATP-binding protein FbpC, (3Fvq); FtsK, DNA translocase FtsK, (2Iut); G40P, ATPase domain of G40P, (3Bh0); Get3, ATPase Get3, (3Sja); GkDnaC, Geobacillus kaustophilus DnaC, (2Vyf); GsDnaB, Geobacillus stearothermophilus DnaB, (2R6c); IoID, Aquifex Aeolicus ABC transporter, (2Pcj); KaiC, Circadian clock protein kinase KaiC, (3K0e); MalK, maltose/maltodextrin import ATP-binding protein, (2Awn); MipZ, bacterial cell division regulator protein MipZ, (2Xit); MMAA, methylmalonic aciduria type A protein, (2Www); Msb8, Thermotoga maritima Abc transporter ATPp-binding protein, (1Vpl); MutS, DNA mismatch repair protein MutS, (1Ewq); P-gp, multidrug resistance protein Pgp-1, (4F4c); PH0284, Upf0273 Protein Ph0284, (2Dr3); PilT, twitching motility protein PilT, (2Gsz); Psy3, Platinum sensitivity protein 3, (4Dt1); Rad50, Dna Double-Strand Break Repair Rad50 Atpase, (3Qku); Rad51, DNA repair protein Rad51, (1Szp); RadA, DNA repair and recombination protein RadA, (4Dc9); RecA, Recombinase A, (1Mo4); RepA, regulatory protein RepA, (1G8y); Rho, transcription termination factor Rho, (3Ice); Rli1p, translation initiation factor, (3J16); RNT1, regulator of nonsense transcripts 1, (2Wjy); SMC, chromosome partition protein, (4I99); Sso2452, putative uncharacterized protein, (2W0m); T7Gp4, T7 DNA Primase/Helicase, (1Cr1); TK, thymidine kinase, (2Ja1); TrwB, conjugal transfer protein TrwB, (1E9r); V1-ATPase, V-Type sodium ATPase, (3VR4); VirB4, type IV secretory pathway Virb4 components-like protein, (4Ag6); Vps4, vacuolar protein sorting-associated protein 4, (3Eih); XDP, Xpd/Rad3 related DNA helicase, (3Crv).
Mentions: Structural classification based on the ATPase core domain shows that cystovirus P4 proteins are closely related to each other and only distantly related to other P-loop ATPases (Figure 4 and Supplementary Figure S2). They most closely resemble RecA-type ATPases (35), such as ATP synthase-like proteins (RHO, F1-ATPase, etc.), RecA-like proteins (RepA, T7 gp4, etc.) and Rad51-like protein (Rad51, RecA, etc.). Many of these proteins are involved in nucleotide repair and recombination and have similar functional properties to P4 proteins. This indicates that the cystoviral P4 proteins form a distinct subfamily of RecA-type ATPases.Figure 4.

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