PDBsum entry 5e9f

Lyase

PDB id: 5e9f

Contents

Protein chains

507 a.a.

453 a.a.

Metals

_MG ×4

Waters ×65

PDB id:

5e9f

Name:

Lyase

Title:

Structural insights of isocitrate lyases from magnaporthe oryzae

Structure:

Isocitrate lyase. Chain: a, b, c, d. Synonym: icl,isocitrase,isocitratase,methylisocitrate lyase,mica, threo-d(s)-isocitrate glyoxylate-lyase. Engineered: yes

Source:

Magnaporthe oryzae 70-15. Rice blast fungus. Organism_taxid: 242507. Strain: 70-15. Gene: icl1, mgg_04895. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.80Å R-factor: 0.187 R-free: 0.226

Authors:

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

Key ref:

Y.Park et al. (2016). Crystal structure and functional analysis of isocitrate lyases from Magnaporthe oryzae and Fusarium graminearum. J Struct Biol, 194, 395-403. PubMed id: 27016285 DOI: 10.1016/j.jsb.2016.03.019

Date:

15-Oct-15 Release date: 27-Apr-16

Protein chains

P0CT06  (ACEA_MAGO7) -  Isocitrate lyase from Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958)

Seq: 547 a.a.

Struc: 507 a.a.

Protein chain

P0CT06  (ACEA_MAGO7) -  Isocitrate lyase from Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958)

Seq: 547 a.a.

Struc: 453 a.a.

Enzyme reactions

• Enzyme class 2: Chains A, B, C, D: E.C.4.1.3.1 - isocitrate lyase.
• Pathway: Glyoxylate Cycle
• Reaction: D-threo-isocitrate = glyoxylate + succinate
• Enzyme class 3: Chains A, B, C, D: E.C.4.1.3.30 - methylisocitrate lyase.
• Reaction: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jsb.2016.03.019

J Struct Biol 194:395-403 (2016)

PubMed id: 27016285

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

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

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. 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.