3V2K

Crystal structure of ribosome inactivating protein from momordica balsamina complexed with the product of RNA substrate adenosine triphosphate at 2.0 A resolution

Summary for 3V2K

• Entry DOI: 10.2210/pdb3v2k/pdb
• Related: 1AHA
• Descriptor: Ribosome inactivating protein, 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ... (5 entities in total)
• Functional Keywords: rip, rna n-glycosidase, plant protein, ribose, inactivation, nitrogenous base, rna, hydrolase
• Biological source: Momordica balsamina (Bitter gourd)
• Total number of polymer chains: 1
• Total formula weight: 27542.19

Authors

Kushwaha, G.S.,Pandey, N.,Sinha, M.,Bhushan, A.,Kaur, P.,Sharma, S.,Singh, T.P. (deposition date: 2011-12-12, release date: 2012-01-18, Last modification date: 2024-11-06)

Primary citation

Kushwaha, G.S.,Pandey, N.,Sinha, M.,Singh, S.B.,Kaur, P.,Sharma, S.,Singh, T.P.
Crystal structures of a type-1 ribosome inactivating protein from Momordica balsamina in the bound and unbound states.
Biochim.Biophys.Acta, 1824:679-691, 2012

PubMed Abstract: The ribosome inactivating proteins (RIPs) of type 1 are plant toxins that eliminate adenine base selectively from the single stranded loop of rRNA. We report six crystal structures, type 1 RIP from Momordica balsamina (A), three in complexed states with ribose (B), guanine (C) and adenine (D) and two structures of MbRIP-1 when crystallized with adenosine triphosphate (ATP) (E) and 2'-deoxyadenosine triphosphate (2'-dATP) (F). These were determined at 1.67Å, 1.60Å, 2.20Å, 1.70Å, 2.07Å and 1.90Å resolutions respectively. The structures contained, (A) unbound protein molecule, (B) one protein molecule and one ribose sugar, (C) one protein molecule and one guanine base, (D) one protein molecule and one adenine base, (E) one protein molecule and one ATP-product adenine molecule and (F) one protein molecule and one 2'-dATP-product adenine molecule. Three distinct conformations of the side chain of Tyr70 were observed with (i) χ(1)=-66°and χ(2)=165° in structures (A) and (B); (ii) χ(1)=-95° and χ(2)=70° in structures (C), (D) and (E); and (iii) χ(1)=-163° and χ(2)=87° in structure (F). The conformation of Tyr70 in (F) corresponds to the structure of a conformational intermediate. This is the first structure which demonstrates that the slow conversion of DNA substrates by RIPs can be trapped during crystallization.

PubMed: 22361570
DOI: 10.1016/j.bbapap.2012.02.005

Experimental method

X-RAY DIFFRACTION (2.07 Å)