A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and...

Area of Science:

• Biochemistry
• Structural Biology
• Microbiology

Background:

• Polynucleotide phosphorylase (PNPase) is crucial for mRNA degradation in prokaryotes.
• Streptomyces antibioticus PNPase exhibits dual activity as both a nucleotidyl transferase and a guanosine 3 '-diphosphate 5 '-triphosphate (pppGpp) synthetase.
• PNPase may coordinate mRNA lifetimes with pppGpp levels during the Streptomyces lifecycle.

Purpose of the Study:

• To determine the three-dimensional structure of Streptomyces antibioticus PNPase.
• To elucidate the structural basis for PNPase trimer assembly and active site organization.
• To understand the structural mechanisms underlying PNPase's dual enzymatic functions.

Main Methods:

• X-ray crystallography was employed to determine the structure of S. antibioticus PNPase.
• The structure was solved in the presence of a phosphate analog, tungstate, bound to the catalytic sites.
• Structure-based sequence analysis was used to identify potential active sites.

Main Results:

• The crystal structure reveals PNPase as a trimeric, multidomain protein with a central channel.
• A novel duplicated architecture forms the structural core, with distinct domains housing the PNPase and pppGpp synthetase active sites.
• The tungstate derivative structure visualizes the PNPase active site within the second core domain.

Conclusions:

• This is the first reported structure of a PNPase, providing a foundation for understanding its assembly and function.
• The structure reveals the arrangement of RNA binding domains and identifies likely catalytic residues for PNPase activity.
• The trimer channel may contribute to processive RNA degradation and regulation by RNA structural elements.