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Updated: Oct 11, 2025
Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
Published on: June 11, 2015
Structure and mutation analysis of the hexameric P4 from Pseudomonas aeruginosa phage phiYY
Caiying Zhang1, Yuelong Li2, Abdus Samad2
1Department 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.
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.
Insights
The P4 protein from Pseudomonas aeruginosa phage phiYY undergoes significant structural changes upon ligand binding, impacting its ATPase activity. Mutations affecting the ligand-binding pocket abolish this activity, while C-terminal truncation does not.
Area of Science:
- Structural biology
- Virology
- Biochemistry
Background:
- Pseudomonas aeruginosa phage phiYY possesses a P4 protein with NTPase activity essential for viral genome packaging.
- Previous studies highlight sequence, structural, and biochemical diversity among P4 proteins from related phages.
Purpose of the Study:
- To elucidate the structure-function relationship of the phiYY P4 protein.
- To investigate the impact of ligand binding and specific mutations on P4 protein activity.
Main Methods:
- Determined four crystal structures of phiYY P4 (apo-form and ligand-bound) at resolutions up to 1.85 Å.
- Performed site-directed mutagenesis, including a four-residue mutation in the ligand-binding pocket and C-terminal truncation.
Main Results:
- Observed significant conformational changes in the H1 motif upon ligand binding compared to the apo-form.
- A four-residue mutation in the ligand-binding pocket completely abolished ATPase activity.
- C-terminal truncation of 50 residues did not affect hexamerization or ATP hydrolysis.
Conclusions:
- Ligand binding induces critical conformational changes in phiYY P4, modulating its NTPase function.
- The ligand-binding pocket and its residues are crucial for P4 ATPase activity.
- The C-terminus is not essential for hexamerization or ATP hydrolysis in phiYY P4.
