6LOZ

crystal structure of alpha-momorcharin in complex with adenine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.202 

wwPDB Validation   3D Report Full Report



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

  • 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 ...

    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; Department of Biology, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, IL 60616, USA. Electronic address: jint@ustc.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome-inactivating protein momordin IA286Momordica charantiaMutation(s): 0 
EC: 3.2.2.22
Find proteins for P16094 (Momordica charantia)
Explore P16094 
Go to UniProtKB:  P16094
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ADE
Query on ADE

Download CCD File 
A
ADENINE
C5 H5 N5
GFFGJBXGBJISGV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.202 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.167α = 90
b = 131.167β = 90
c = 37.145γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2020-01-07 
  • Released Date: 2020-11-18 
  • Deposition Author(s): Fan, X., Jin, T.

Revision History 

  • Version 1.0: 2020-11-18
    Type: Initial release