8DKR

Pseudomonas-phage E217 TerL nuclease domain

  • Classification: HYDROLASE
  • Organism(s): Pseudomonas phage vB_PaeM_E217
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-07-06 Released: 2022-09-07 
  • Deposition Author(s): Cingolani, G., Lokareddy, R., Hou, D.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Office of the Director, National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Terminase Subunits from the Pseudomonas-Phage E217.

Lokareddy, R.K.Hou, C.D.Doll, S.G.Li, F.Gillilan, R.E.Forti, F.Horner, D.S.Briani, F.Cingolani, G.

(2022) J Mol Biol 434: 167799-167799

  • DOI: https://doi.org/10.1016/j.jmb.2022.167799
  • Primary Citation of Related Structures:  
    7UXE, 8DKR

  • PubMed Abstract: 

    Pseudomonas phages are increasingly important biomedicines for phage therapy, but little is known about how these viruses package DNA. This paper explores the terminase subunits from the Myoviridae E217, a Pseudomonas-phage used in an experimental cocktail to eradicate P. aeruginosa in vitro and in animal models. We identified the large (TerL) and small (TerS) terminase subunits in two genes ∼58 kbs away from each other in the E217 genome. TerL presents a classical two-domain architecture, consisting of an N-terminal ATPase and C-terminal nuclease domain arranged into a bean-shaped tertiary structure. A 2.05 Å crystal structure of the C-terminal domain revealed an RNase H-like fold with two magnesium ions in the nuclease active site. Mutations in TerL residues involved in magnesium coordination had a dominant-negative effect on phage growth. However, the two ions identified in the active site were too far from each other to promote two-metal-ion catalysis, suggesting a conformational change is required for nuclease activity. We also determined a 3.38 Å cryo-EM reconstruction of E217 TerS that revealed a ring-like decamer, departing from the most common nonameric quaternary structure observed thus far. E217 TerS contains both N-terminal helix-turn-helix motifs enriched in basic residues and a central channel lined with basic residues large enough to accommodate double-stranded DNA. Overexpression of TerS caused a more than a 4-fold reduction of E217 burst size, suggesting a catalytic amount of the protein is required for packaging. Together, these data expand the molecular repertoire of viral terminase subunits to Pseudomonas-phages used for phage therapy.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Large terminase proteinA [auth B],
B [auth A]
255Pseudomonas phage vB_PaeM_E217Mutation(s): 0 
Gene Names: vBPaeME217_00005
EC: 3.1
UniProt
Find proteins for A0A2K8HL37 (Pseudomonas phage vB_PaeM_E217)
Explore A0A2K8HL37 
Go to UniProtKB:  A0A2K8HL37
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K8HL37
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.601α = 90
b = 62.628β = 90
c = 149.253γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM100888
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM140733
National Institutes of Health/Office of the DirectorUnited StatesOD017987
National Institutes of Health/Office of the DirectorUnited StatesOD023479
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA56036

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-07
    Type: Initial release
  • Version 1.1: 2022-09-14
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description