1yf8
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Crystal structure of Himalayan mistletoe RIP reveals the presence of a natural inhibitor and a new functionally active sugar-binding site
OverviewOverview
Ribosome-inactivating proteins (RIPs) are toxins involved in plant, defense. How the plant prevents autotoxicity is not yet fully understood., The present study is the first structural evidence of a naturally, inhibited form of RIP from a plant. Himalayan mistletoe RIP (HmRIP) was, purified from Viscum album leaves and crystallized with lactose. The, structure was determined by the molecular replacement method and refined, at 2.8-A resolution. The crystal structure revealed the presence of high, quality non-protein electron density at the active site, into which a, pteridine derivative (2-amino 4-isopropyl 6-carboxyl pteridine) was, modeled. The carboxyl group of the ligand binds strongly with the key, active site residue Arg(162), nullifies the positive charge required for, catalysis, and thereby acts as a natural inhibitor. Lectin subunits of, RIPs have two active sugar-binding sites present in 1alpha- and, 2gamma-subdomains. A third functionally active site has been identified in, the 1beta-subdomain of HmRIP. The 1beta-site is active despite the absence, of conserved polar sugar-binding residues. Loss of these residues is, compensated by the following: (i) the presence of an extended site where, the penultimate sugar also interacts with the protein; (ii) the, interactions of galactose with the protein main chain carbonyl and amide, nitrogen atoms; (iii) the presence of a well defined pocket encircled by, four walls; and (iv) a favorable stacking of the galactose ring with, Tyr(66) besides the conserved Phe(75). The mode of sugar binding is also, distinct at the 1alpha and 2gamma sugar-binding sites.
About this StructureAbout this Structure
1YF8 is a Protein complex structure of sequences from Viscum album with NAG, GAL and P6C as ligands. Active as rRNA N-glycosylase, with EC number 3.2.2.22 Full crystallographic information is available from OCA.
ReferenceReference
Crystal structure of himalayan mistletoe ribosome-inactivating protein reveals the presence of a natural inhibitor and a new functionally active sugar-binding site., Mishra V, Bilgrami S, Sharma RS, Kaur P, Yadav S, Krauspenhaar R, Betzel C, Voelter W, Babu CR, Singh TP, J Biol Chem. 2005 May 27;280(21):20712-21. Epub 2005 Mar 17. PMID:15774467
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