6MV7

Crystal structure of RNAse 6

Summary for 6MV7

• Entry DOI: 10.2210/pdb6mv7/pdb
• Descriptor: Ribonuclease K6, ADENOSINE MONOPHOSPHATE (3 entities in total)
• Functional Keywords: rnase, nuclease, hydrolase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 15154.29

Authors

Couture, J.-F.,Doucet, N. (deposition date: 2018-10-24, release date: 2019-11-13, Last modification date: 2024-11-06)

Primary citation

Narayanan, C.,Bernard, D.N.,Letourneau, M.,Gagnon, J.,Gagne, D.,Bafna, K.,Calmettes, C.,Couture, J.F.,Agarwal, P.K.,Doucet, N.
Insights into Structural and Dynamical Changes Experienced by Human RNase 6 upon Ligand Binding.
Biochemistry, 59:755-765, 2020

PubMed Abstract: Ribonuclease 6 (RNase 6) is one of eight catalytically active human pancreatic-type RNases that belong to a superfamily of rapidly evolving enzymes. Like some of its human homologues, RNase 6 exhibits host defense properties such as antiviral and antibacterial activities. Recently solved crystal structures of this enzyme in its nucleotide-free form show the conservation of the prototypical kidney-shaped fold preserved among vertebrate RNases, in addition to revealing the presence of a unique secondary active site. In this study, we determine the structural and conformational properties experienced by RNase 6 upon binding to substrate and product analogues. We present the first crystal structures of RNase 6 bound to a nucleotide ligand (adenosine 5'-monophosphate), in addition to RNase 6 bound to phosphate ions. While the enzyme preserves B subsite ligand preferences, our results show a lack of typical B subsite interactions normally observed in homologous ligand-bound RNases. A comparison of the dynamical properties of RNase 6 in its apo-, substrate-, and product-bound states highlight the unique dynamical properties experienced on time scales ranging from nano- to milliseconds. Overall, our results confirm the specific evolutionary adaptation of RNase 6 relative to its unique catalytic and biological activities.

PubMed: 31909602
DOI: 10.1021/acs.biochem.9b00888

Experimental method

X-RAY DIFFRACTION (2.59 Å)