6LOY

crystal structure of alpha-momorcharin in complex with dAMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.349 
  • R-Value Work: 0.300 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Atomic-resolution structures of type I ribosome inactivating protein alpha-momorcharin with different substrate analogs.

Fan, X.Wang, Y.Guo, F.Zhang, Y.Jin, T.

(2020) Int J Biol Macromol 164: 265-276

  • DOI: https://doi.org/10.1016/j.ijbiomac.2020.07.063
  • Primary Citation of Related Structures:  
    6LOQ, 6LOR, 6LOV, 6LOW, 6LOY, 6LOZ, 6LP0

  • 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.


  • Organizational Affiliation

    Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China; Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome-inactivating protein momordin I286Momordica charantiaMutation(s): 0 
EC: 3.2.2.22
UniProt
Find proteins for P16094 (Momordica charantia)
Explore P16094 
Go to UniProtKB:  P16094
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16094
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D5M (Subject of Investigation/LOI)
Query on D5M

Download Ideal Coordinates CCD File 
B [auth A]2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O6 P
KHWCHTKSEGGWEX-RRKCRQDMSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.349 
  • R-Value Work: 0.300 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.667α = 90
b = 130.667β = 90
c = 39.23γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description