Molecular switch-like regulation enables global subunit coordination in a viral ring ATPase

Tafoya, Sara; Liu, Shixin; Castillo, Juan P.; Atz, Rockney; Morais, Marc C.; Grimes, Shelley; Jardine, Paul J.; Bustamante, Carlos

doi:10.1073/pnas.1802736115

Cited by 32 publications

(56 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Also, both the N-and C-terminal domains appear to interact with incoming DNA (Figures 3, 4), again differing from results for T4 that suggest only the CTD interacts with DNA (51). Additionally, all five NTDs and CTDs appear to interact with DNA, in contrast to previous results we reported that only one subunit contacts the DNA (35). Further, the DNA structure differs considerably from canonical B-form DNA.…”

Section: Symmetry Breaking Prna-atpase Structurecontrasting

confidence: 84%

“…Based on sequence alignment with members of the FtsK branch of the ASCE superfamily, R146 was predicted to be the canonical ATPase 'arginine finger'. This prediction was supported by biochemical experiments designed to report trans-acting activity (31,35). While the current structural data could support R146 acting as the arginine finger, K105 seems equally well, if not better, positioned to assume this role.…”

Section: Figure 6 Domain Linker and Trans-acting Residues: (A) Sidevsupporting

confidence: 56%

“…Hence, while R146 likely does act in trans during nucleotide cycling, assigning it the catalytic-trigger role of the arginine finger may be premature. Indeed, single molecule optical laser tweezer experiments suggest the R146 may play a role in nucleotide exchange (35), thus explaining the reported trans-activity while allowing for the possibility that K105 could function as the catalytic 'arginine' finger in gp16. Of note, in addition to closing over the active site, the linker interacts with the edge of the sheet in the trans-acting subunit where R146 and K105 reside ( Figures 6B, D), consistent with potential roles in coordinating either/both ATP hydrolysis and nucleotide exchange in adjacent subunits.…”

Section: Figure 6 Domain Linker and Trans-acting Residues: (A) Sidevmentioning

confidence: 99%

“…Single molecule experiments have shown that nucleotide exchange occurs sequentially and is highly coordinated, with one subunit completing exchange of ADP for ATP prior to exchange in the next subunit (33,35) (Figure 1B). The order of nucleotide exchange around the ring could occur in either the same or opposite direction as hydrolysis.…”

Section: Mechanism Of Translocationmentioning

confidence: 99%

“…No DNA translocation occurs during the subsequent dwell phase, when all five gp16 subunits release ADP from the previous hydrolysis cycle and load ATP in an interlaced manner. More recent optical laser tweezer experiments show that nucleotide exchange during the dwell is coordinated between adjacent subunits, and that the order of exchange is influenced by subunit interactions with DNA (35). Using altered DNA substrates, additional single molecule experiments indicate that the motor makes two types of contact with the translocating DNA (36).…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

A viral genome packaging motor transitions between cyclic and helical symmetry to translocate dsDNA

Woodson¹,

Pajak

Wang

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Molecular segregation and biopolymer manipulation require the action of molecular motors to do work by applying directional forces to macromolecules. The additional strand conserved E (ASCE) ring motors are an ancient family of molecular motors responsible for diverse tasks ranging from biological polymer manipulation (e.g. protein degradation and chromosome segregation) to establishing and maintaining proton gradients across mitochondrial membranes. Viruses also utilize ASCE segregation motors to package their genomes into their protein capsids and serve as accessible experimental systems due to their relative simplicity. We show by CryoEM focused image reconstruction that ASCE ATPases in viral dsDNA packaging motors adopt helical symmetry complementary to their dsDNA substrates. Together with previous data, including structural results showing these ATPases in planar ring conformations, our results suggest that these motors cycle between helical and planar cyclical symmetry, providing a possible mechanism for directional translocation of DNA. We further note that similar changes in quaternary structure have been observed for proteasome and helicase motors, suggesting an ancient and common mechanism of force generation that has been adapted for specific tasks over the course of evolution.

show abstract

Section: Symmetry Breaking Prna-atpase Structurecontrasting

confidence: 84%

Section: Figure 6 Domain Linker and Trans-acting Residues: (A) Sidevsupporting

confidence: 56%

Section: Figure 6 Domain Linker and Trans-acting Residues: (A) Sidevmentioning

confidence: 99%

Section: Mechanism Of Translocationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

A viral genome packaging motor transitions between cyclic and helical symmetry to translocate dsDNA

Woodson¹,

Pajak

Wang

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

Revolving ATPase motors as asymmetrical hexamers in translocating lengthy dsDNA via conformational changes and electrostatic interactions in phi29, T7, herpesvirus, mimivirus, E. coli, and Streptomyces

2023

View full text Add to dashboard Cite

Investigations of the parallel architectures of biomotors in both prokaryotic and eukaryotic systems suggest a similar revolving mechanism in the use of ATP to drive translocation of the lengthy double‐stranded (ds)DNA genomes. This mechanism is exemplified by the dsDNA packaging motor of bacteriophage phi29 that operates through revolving but not rotating dsDNA to “Push through a one‐way valve”. This unique and novel revolving mechanism discovered in phi29 DNA packaging motor was recently reported in other systems including the dsDNA packaging motor of herpesvirus, the dsDNA ejecting motor of bacteriophage T7, the plasmid conjugation machine TraB in Streptomyces, the dsDNA translocase FtsK of gram‐negative bacteria, and the genome‐packaging motor in mimivirus. These motors exhibit an asymmetrical hexameric structure for transporting the genome via an inch‐worm sequential action. This review intends to delineate the revolving mechanism from a perspective of conformational changes and electrostatic interactions. In phi29, the positively charged residues Arg‐Lys‐Arg in the N‐terminus of the connector bind the negatively charged interlocking domain of pRNA. ATP binding to an ATPase subunit induces the closed conformation of the ATPase. The ATPase associates with an adjacent subunit to form a dimer facilitated by the positively charged arginine finger. The ATP‐binding induces a positive charging on its DNA binding surface via an allostery mechanism and thus the higher affinity for the negatively charged dsDNA. ATP hydrolysis induces an expanded conformation of the ATPase with a lower affinity for dsDNA due to the change of the surface charge, but the (ADP+Pi)‐bound subunit in the dimer undergoes a conformational change that repels dsDNA. The positively charged lysine rings of the connector attract dsDNA stepwise and periodically to keep its revolving motion along the channel wall, thus maintaining the one‐way translocation of dsDNA without reversal and sliding out. The finding of the presence of the asymmetrical hexameric architectures of many ATPases that use the revolving mechanism may provide insights into the understanding of translocation of the gigantic genomes including chromosomes in complicated systems without coiling and tangling to speed up dsDNA translocation and save energy.

show abstract

Viral Genomic DNA Packaging Machinery

Hawkins,

Godwin,

Antson

2024

Subcellular Biochemistry

View full text Add to dashboard Cite

Molecular switch-like regulation enables global subunit coordination in a viral ring ATPase

Cited by 32 publications

References 19 publications

A viral genome packaging motor transitions between cyclic and helical symmetry to translocate dsDNA

A viral genome packaging motor transitions between cyclic and helical symmetry to translocate dsDNA

Revolving ATPase motors as asymmetrical hexamers in translocating lengthy dsDNA via conformational changes and electrostatic interactions in phi29, T7, herpesvirus, mimivirus, E. coli, and Streptomyces

Viral Genomic DNA Packaging Machinery

Contact Info

Product

Resources

About