7KS4

Thermus Phage P74-26 Large Terminase ATPase domain with partially bound ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Viral packaging ATPases utilize a glutamate switch to couple ATPase activity and DNA translocation.

Pajak, J.Atz, R.Hilbert, B.J.Morais, M.C.Kelch, B.A.Jardine, P.J.Arya, G.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: 10.1073/pnas.2024928118
  • Primary Citation of Related Structures:  
    7KS4

  • PubMed Abstract: 
  • Many viruses utilize ringed packaging ATPases to translocate double-stranded DNA into procapsids during replication. A critical step in the mechanochemical cycle of such ATPases is ATP binding, which causes a subunit within the motor to grip DNA tightly. Here, we probe the underlying molecular mechanism by which ATP binding is coupled to DNA gripping and show that a glutamate-switch residue found in AAA+ enzymes is central to this coupling in viral packaging ATPases ...

    Many viruses utilize ringed packaging ATPases to translocate double-stranded DNA into procapsids during replication. A critical step in the mechanochemical cycle of such ATPases is ATP binding, which causes a subunit within the motor to grip DNA tightly. Here, we probe the underlying molecular mechanism by which ATP binding is coupled to DNA gripping and show that a glutamate-switch residue found in AAA+ enzymes is central to this coupling in viral packaging ATPases. Using free-energy landscapes computed through molecular dynamics simulations, we determined the stable conformational state of the ATPase active site in ATP- and ADP-bound states. Our results show that the catalytic glutamate residue transitions from an active to an inactive pose upon ATP hydrolysis and that a residue assigned as the glutamate switch is necessary for regulating this transition. Furthermore, we identified via mutual information analyses the intramolecular signaling pathway mediated by the glutamate switch that is responsible for coupling ATP binding to conformational transitions of DNA-gripping motifs. We corroborated these predictions with both structural and functional experimental measurements. Specifically, we showed that the crystal structure of the ADP-bound P74-26 packaging ATPase is consistent with the structural coupling predicted from simulations, and we further showed that disrupting the predicted signaling pathway indeed decouples ATPase activity from DNA translocation activity in the φ29 DNA packaging motor. Our work thus establishes a signaling pathway that couples chemical and mechanical events in viral DNA packaging motors.


    Organizational Affiliation

    Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708; gaurav.arya@duke.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phage terminase large subunitA [auth B]274Thermus virus P74-26Mutation(s): 0 
Gene Names: P74p84
UniProt
Find proteins for A7XXR1 (Thermus virus P74-26)
Explore A7XXR1 
Go to UniProtKB:  A7XXR1
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.515α = 90
b = 129.515β = 90
c = 129.515γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-05
    Type: Initial release