4EMF

Crystal structure of the complex of type I Ribosome inactivating protein in complex with 7n-methyl-8-hydroguanosine-5-p-diphosphate at 1.77 A

Summary for 4EMF

• Entry DOI: 10.2210/pdb4emf/pdb
• Related: 3S9Q
• Descriptor: rRNA N-glycosidase, GLYCEROL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (5 entities in total)
• Functional Keywords: ligand binding, hydrolase, ribosome inactivating protein, complex hydrolase
• Biological source: Momordica balsamina (Bitter gourd)
• Total number of polymer chains: 1
• Total formula weight: 27957.39

Authors

Yamini, S.,Kushwaha, G.S.,Sinha, M.,Kaur, P.,Sharma, S.,Singh, T.P. (deposition date: 2012-04-12, release date: 2012-05-02, Last modification date: 2024-11-06)

Primary citation

Kushwaha, G.S.,Yamini, S.,Kumar, M.,Sinha, M.,Kaur, P.,Sharma, S.,Singh, T.P.
First structural evidence of sequestration of mRNA cap structures by type 1 ribosome inactivating protein from Momordica balsamina.
Proteins, 81:896-905, 2013

PubMed Abstract: This is the first structural evidence of recognition of mRNA cap structures by a ribosome inactivating protein. It is well known that a unique cap structure is formed at the 5' end of mRNA for carrying out various processes including mRNA maturation, translation initiation, and RNA turnover. The binding studies and crystal structure determinations of type 1 ribosome inactivating protein (RIP-1) from Momordica balsamina (MbRIP-1) were carried out with mRNA cap structures including (i) N7-methyl guanine (m7G), (ii) N7-methyl guanosine diphosphate (m7GDP), and (iii) N7-methyl guanosine triphosphate (m7GTP). These compounds showed affinities to MbRIP-1 at nanomolar concentrations. The structure determinations of the complexes of MbRIP-1 with m7G, m7GDP, and m7GTP at 2.65, 1.77, and 1.75 Å resolutions revealed that all the three compounds bound to MbRIP-1 in the substrate binding site at the positions which are slightly shifted towards Glu85 as compared to those of rRNA substrates. In this position, Glu85 forms several hydrogen bonds with guanine moiety while N-7 methyl group forms van der Waals contacts. However, the guanine rings are poorly stacked in these complexes. Thus, the mode of binding by MbRIP-1 to mRNA cap structures is different which results in the inhibition of depurination. Since some viruses are known to exploit the capping property of the host, this action of MbRIP-1 may have implications for the antiviral activity of this protein in vivo. The understanding of the mode of binding of MbRIP-1 to cap structures may also assist in the design of anti-viral agents.

PubMed: 23280611
DOI: 10.1002/prot.24248

Experimental method

X-RAY DIFFRACTION (1.77 Å)