7ESO

Structure and mutation analysis of the hexameric P4 from Pseudomonas aeruginosa phage phiYY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and mutation analysis of the hexameric P4 from Pseudomonas aeruginosa phage phiYY.

Zhang, C.Li, Y.Samad, A.Zheng, P.Ji, Z.Chen, F.Zhang, H.Jin, T.

(2022) Int J Biol Macromol 194: 42-49

  • DOI: https://doi.org/10.1016/j.ijbiomac.2021.11.129
  • Primary Citation of Related Structures:  
    7ESO, 7ESP, 7ESQ, 7ESV

  • PubMed Abstract: 

    phiYY is a foremost member of Cystoviridae isolated from Pseudomonas aeruginosa. Its P4 protein with NTPase activity is a molecular motor for their genome packing during viral particle assembly. Previously studies on the P4 from four Pseudomonas phages phi6, phi8, phi12 and phi13 reveal that despite of belonging to the same protein family, they are unique in sequence, structure and biochemical properties. To better understand the structure and function of phiYY P4, four crystal structures of phiYY P4 in apo-form or combined with different ligands were solved at the resolution between 1.85 Å and 2.43 Å, which showed drastic conformation change of the H1 motif in ligand-bound forms compared with in apo-form, a four residue-mutation at the ligand binding pocket abolished its ATPase activity. Furthermore, the truncation mutation of the 50 residues at the C-terminal did not impair the hexamerization and ATP hydrolysis.


  • Organizational Affiliation

    Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Packaging NTPase354Pseudomonas phage phiYYMutation(s): 0 
Gene Names: phiYY_sL4
UniProt
Find proteins for A0A1U9AK63 (Pseudomonas phage phiYY)
Explore A0A1U9AK63 
Go to UniProtKB:  A0A1U9AK63
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1U9AK63
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 241.075α = 90
b = 241.075β = 90
c = 152.95γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description