1IYB

Crystal Structure of the Nicotiana glutinosa Ribonuclease NW

Summary for 1IYB

• Entry DOI: 10.2210/pdb1iyb/pdb
• Descriptor: Ribonuclease, GUANOSINE-5'-MONOPHOSPHATE (3 entities in total)
• Functional Keywords: hydrolase, ribonuclease
• Biological source: Nicotiana glutinosa
• Total number of polymer chains: 2
• Total formula weight: 46979.38

Authors

Kawano, S.,Kakuta, Y.,Kimura, M. (deposition date: 2002-08-05, release date: 2003-08-05, Last modification date: 2024-11-20)

Primary citation

Kawano, S.,Kakuta, Y.,Kimura, M.
Guanine binding site of the Nicotiana glutinosa ribonuclease NW revealed by X-ray crystallography
Biochemistry, 41:15195-15202, 2002

PubMed Abstract: Ribonuclease NW (RNase NW), the wound-inducible RNase in Nicotiana glutinosa leaves, preferentially cleaves guanylic acid. We expressed the cDNA encoding RNase NW in the methylotrophic yeast Pichia pastoris using the expression vector pPIC9K, and the resulting recombinant RNase NW (ryRNaseNW) secreted into medium was purified to apparent homogeneity using column chromatography. The crystal structure of ryRNase NW bound to 5'-GMP was determined at 1.5 A resolution by molecular replacement with tomato RNase LE as a search model. The RNase NW structurally belongs to the (alpha + beta) class of proteins, having eight helices (five alpha-helices and three 3(10) helices) and six beta-strands, and its structure is highly similar to those of other plant RNases, including a uridylic acid preferential RNase MC1 from bitter gourd seeds. The guanine ring of 5'-GMP lies in a hydrophobic pocket of the molecular surface composed of Tyr17, Tyr71, Ala80, Leu79, and Phe89: the guanine base is sandwiched between aromatic side chains of Tyr17 and Phe89. In addition, the guanine base is firmly stabilized by a network of hydrogen bonds of the side chains of Gln12 and Thr78, as well as of the main chain of Leu79. Therefore, Gln12, Tyr17, Thr78, Leu79, and Phe89 are responsible for recognition of the guanine base by RNase NW, findings which provide insight into the manner in which RNase NW preferentially cleaves guanylic acid.

PubMed: 12484757
DOI: 10.1021/bi026247l

Experimental method

X-RAY DIFFRACTION (1.5 Å)