6LP0

crystal structure of alpha-momorcharin in complex with AMP

Summary for 6LP0

• Entry DOI: 10.2210/pdb6lp0/pdb
• Descriptor: Ribosome-inactivating protein momordin I, ADENOSINE MONOPHOSPHATE, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (4 entities in total)
• Functional Keywords: alpha-momorcharin, ribosome-inactivating protein, rrna n-glycosidase, amp, plant protein
• Biological source: Momordica charantia (Bitter gourd)
• Total number of polymer chains: 1
• Total formula weight: 32131.39

Authors

Fan, X.,Jin, T. (deposition date: 2020-01-07, release date: 2020-11-18, Last modification date: 2023-11-29)

Primary citation

Fan, X.,Wang, Y.,Guo, F.,Zhang, Y.,Jin, T.
Atomic-resolution structures of type I ribosome inactivating protein alpha-momorcharin with different substrate analogs.
Int.J.Biol.Macromol., 164:265-276, 2020

PubMed Abstract: Alpha-momorcharin (Alpha-MMC) from the seed of bitter melon is a type I ribosome inactivating protein (RIP) that removes a specific adenine from 28S rRNA and inhibits protein biosynthesis. Here, we report seven crystal complex structures of alpha-MMC with different substrate analogs (adenine, AMP, cAMP, dAMP, ADP, GMP, and xanthosine) at 1.08 Å to 1.52 Å resolution. These structures reveal that not only adenine, but also guanine and their analogs can effectively bind to alpha-MMC. The side chain of Tyr93 adopts two conformations, serving as a switch to open and close the substrate binding pocket of alpha-MMC. Although adenine, AMP, GMP, and guanine are located in a similar active site in different RIPs, residues involved in the interaction between RIPs and substrate analogs are slightly different. Complex structures of alpha-MMC with different substrate analogs solved in this study provide useful information on its enzymatic mechanisms and may enable the development of new inhibitors to treat the poisoning of alpha-MMC.

PubMed: 32653369
DOI: 10.1016/j.ijbiomac.2020.07.063

Experimental method

X-RAY DIFFRACTION (1.519 Å)