Characterization of an RNase with two catalytic centers. Human RNase6 catalytic and phosphate-binding site arrangement favors the endonuclease cleavage of polymeric substrates

Guillem Prats-Ejarque, Jose A. Blanco, Vivian A. Salazar, Victòria M. Nogués, Mohammed Moussaoui, Ester Boix

Research output: Contribution to journalArticleResearch

6 Citations (Scopus)

Abstract

© 2018 Elsevier B.V. Background: Human RNase6 is a small cationic antimicrobial protein that belongs to the vertebrate RNaseA superfamily. All members share a common catalytic mechanism, which involves a conserved catalytic triad, constituted by two histidines and a lysine (His15/His122/Lys38 in RNase6 corresponding to His12/His119/Lys41 in RNaseA). Recently, our first crystal structure of human RNase6 identified an additional His pair (His36/His39) and suggested the presence of a secondary active site. Methods: In this work we have explored RNase6 and RNaseA subsite architecture by X-ray crystallography, site-directed mutagenesis and kinetic characterization. Results: The analysis of two novel crystal structures of RNase6 in complex with phosphate anions at atomic resolution locates a total of nine binding sites and reveals the contribution of Lys87 to phosphate-binding at the secondary active center. Contribution of the second catalytic triad residues to the enzyme activity is confirmed by mutagenesis. RNase6 catalytic site architecture has been compared with an RNaseA engineered variant where a phosphate-binding subsite is converted into a secondary catalytic center (RNaseA-K7H/R10H). Conclusions: We have identified the residues that participate in RNase6 second catalytic triad (His36/His39/Lys87) and secondary phosphate-binding sites. To note, residues His39 and Lys87 are unique within higher primates. The RNaseA/RNase6 side-by-side comparison correlates the presence of a dual active site in RNase6 with a favored endonuclease-type cleavage pattern. General significance: An RNase dual catalytic and extended binding site arrangement facilitates the cleavage of polymeric substrates. This is the first report of the presence of two catalytic centers in a single monomer within the RNaseA superfamily.
Original languageEnglish
Pages (from-to)105-117
Number of pages13
JournalBiochimica et Biophysica Acta - General Subjects
Volume1863
Issue number1
DOIs
Publication statusPublished - 1 Jan 2019

Keywords

  • Endoribonuclease
  • Enzymology
  • Protein crystallography
  • RNase6
  • RNaseA
  • Substrate binding site
  • Catalytic Domain
  • Mutagenesis, Site-Directed
  • Phosphates/chemistry
  • Protein Structure, Secondary
  • Humans
  • Ribonuclease, Pancreatic/chemistry
  • Crystallography, X-Ray
  • Histidine/chemistry
  • Polymers/chemistry
  • Endonucleases/chemistry
  • Ribonucleases/chemistry
  • Catalysis
  • Kinetics
  • Mutation
  • Lysine/chemistry
  • Exonucleases/chemistry
  • ACTIVE-SITE
  • SUBSITES
  • ANGSTROM RESOLUTION
  • COMPLEX
  • MECHANISM
  • CRYSTAL-STRUCTURE
  • BOVINE PANCREATIC RIBONUCLEASE
  • EOSINOPHIL CATIONIC PROTEIN
  • EVOLUTION
  • NEUROTOXIN EDN

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