4ZZ6

Structure of the complex of type 1 ribosome inactivating protein from Momordica balsamina with a nucleotide, cytidine triphosphate at 2.0A resolution

Replaces:  4K6S

Summary for 4ZZ6

• Entry DOI: 10.2210/pdb4zz6/pdb
• Descriptor: Ribosome inactivating protein, 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ... (5 entities in total)
• Functional Keywords: hydrolase
• Biological source: Momordica balsamina (Bitter gourd)
• Total number of polymer chains: 1
• Total formula weight: 27982.31

Authors

Yamin, S.,Pandey, S.,Kaur, P.,Sharma, S.,Singh, T.P. (deposition date: 2015-05-22, release date: 2015-06-10, Last modification date: 2024-11-06)

Primary citation

Yamini, S.,Pandey, S.N.,Kaur, P.,Sharma, S.,Singh, T.P.
Binding and structural studies of the complexes of type 1 ribosome inactivating protein fromMomordica balsaminawith cytosine, cytidine, and cytidine diphosphate.
Biochem Biophys Rep, 4:134-140, 2015

PubMed Abstract: The type 1 ribosome inactivating protein from (RIP1) has been shown to interact with purine bases, adenine and guanine of RNA/DNA. We report here the binding and structural studies of RIP1 with a pyrimidine base, cytosine; cytosine containing nucleoside, cytidine; and cytosine containing nucleotide, cytidine diphosphate. All three compounds bound to RIP1 at the active site with dissociation constants of 10 M-10 M. As reported earlier, in the structure of native RIP1, there are 10 water molecules in the substrate binding site. Upon binding of cytosine to RIP1, four water molecules were dislodged from the substrate binding site while five water molecules were dislodged when cytidine bound to RIP1. Seven water molecules were dislocated when cytidine diphosphate bound to RIP1. This showed that cytidine diphosphate occupied a larger space in the substrate binding site enhancing the buried surface area thus making it a relatively better inhibitor of RIP1 as compared to cytosine and cytidine. The key residues involved in the recognition of cytosine, cytidine and cytidine diphosphate were Ile71, Glu85, Tyr111 and Arg163. The orientation of cytosine in the cleft is different from that of adenine or guanine indicating a notable difference in the modes of binding of purine and pyrimidine bases. Since adenine containing nucleosides/nucleotides are suitable substrates, the cytosine containing nucleosides/nucleotides may act as inhibitors.

PubMed: 29124196
DOI: 10.1016/j.bbrep.2015.09.006

Experimental method

X-RAY DIFFRACTION (2 Å)