5E9G

Structural insights of isocitrate lyases from Magnaporthe oryzae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure and functional analysis of isocitrate lyases from Magnaporthe oryzae and Fusarium graminearum

Park, Y.Cho, Y.Lee, Y.-H.Lee, Y.-W.Rhee, S.

(2016) J Struct Biol 194: 395-403

  • DOI: 10.1016/j.jsb.2016.03.019
  • Primary Citation of Related Structures:  
    5E9F, 5E9H, 5E9G

  • PubMed Abstract: 
  • The glyoxylate cycle bypasses a CO2-generating step in the tricarboxylic acid (TCA) cycle and efficiently assimilates C2 compounds into intermediates that can be used in later steps of the TCA cycle. It plays an essential role in pathogen survival during host infection such that the enzymes involved in this cycle have been suggested as potential drug targets against human pathogens ...

    The glyoxylate cycle bypasses a CO2-generating step in the tricarboxylic acid (TCA) cycle and efficiently assimilates C2 compounds into intermediates that can be used in later steps of the TCA cycle. It plays an essential role in pathogen survival during host infection such that the enzymes involved in this cycle have been suggested as potential drug targets against human pathogens. Isocitrate lyase (ICL) catalyzes the first-step reaction of the glyoxylate cycle, using isocitrate from the TCA cycle as the substrate to produce succinate and glyoxylate. In this study we report the crystal structure of Magnaporthe oryzae ICL in both the ligand-free form and as a complex with Mg(2+), glyoxylate, and glycerol, as well as the structure of the Fusarium graminearum ICL complexed with Mn(2+) and malonate. We also describe the ligand-induced conformational changes in the catalytic loop and C-terminal region, both of which are essential for catalysis. Using various mutant ICLs in an activity assay, we gained insight into the function of residues within the active site. These structural and functional analyses provide detailed information with regard to fungal ICLs.


    Organizational Affiliation

    Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea; Center for Fungal Pathogenesis, Seoul National University, Seoul, Republic of Korea. Electronic address: srheesnu@snu.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isocitrate lyase ABCD560Pyricularia oryzae 70-15Mutation(s): 1 
Gene Names: ICL1MGG_04895
EC: 4.1.3.1 (PDB Primary Data), 4.1.3.30 (PDB Primary Data)
Find proteins for P0CT06 (Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958))
Explore P0CT06 
Go to UniProtKB:  P0CT06
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.122α = 90
b = 135.078β = 90
c = 158.704γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-05-18
    Changes: Database references