The nuclease A inhibitor represents a new variation of the rare PR-1 fold.
Nuclease A (NucA) from Anabaena sp. is a non-specific endonuclease able to degrade single and double-stranded DNA and RNA. The endonucleolytic activity is inhibited by the nuclease A inhibitor (NuiA), which binds to NucA with 1:1 stoichiometry and picomolar affinity. In order to better understand the mechanism of inhibition, the solution structure of NuiA was determined by NMR methods. The fold of NuiA is an alpha-beta-alpha sandwich but standard database searches by DALI and TOP revealed no structural homologies. A visual inspection of alpha-beta-alpha folds in the CATH database revealed similarities to the PR-1-like fold (SCOP nomenclature). The similarities include the ordering of secondary structural elements, a single helix on one face of the alpha-beta-alpha sandwich, and three helices on the other face. However, a major difference is in the IV helix, which in the PR-1 fold is short and perpendicular to the I and III helices, but in NuiA is long and parallel to the I and III helices. Additionally, a strand insertion in the beta-sheet makes the NuiA beta-sheet completely antiparallel in organization. The fast time-scale motions of NuiA, characterized by enhanced flexibility of the extended loop between helices III and IV, also show similarities to P14a, which is a PR-1 fold. We propose that the purpose of the PR-1 fold is to form a stable scaffold to present this extended structure for biological interactions with other proteins. This hypothesis is supported by data that show that when NuiA is bound to NucA significant changes in chemical shift occur in the extended loop between helices III and IV.
Kirby
Thomas W
TW
National Institute of Environmental Health Sciences, P.O. Box 12233, MD MR-01, Research Triangle Park, NC 27709, USA.
Mueller
Geoffrey A
GA
DeRose
Eugene F
EF
Lebetkin
Mark S
MS
Meiss
Gregor
G
Pingoud
Alfred
A
London
Robert E
RE
D017033:Anabaena / Q000201:enzymology; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D004706:Endodeoxyribonucleases / Q000037:antagonists & inhibitors*; D004720:Endonucleases / Q000737:chemistry*; D004722:Endoribonucleases / Q000037:antagonists & inhibitors*; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011485:Protein Binding; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
D001426:Bacterial Proteins; C106206:NuiA protein, Anabaena; D004706:Endodeoxyribonucleases; D004720:Endonucleases; D004722:Endoribonucleases; C085858:sugar-nonspecific nuclease