1DQU

CRYSTAL STRUCTURE OF THE ISOCITRATE LYASE FROM ASPERGILLUS NIDULANS

• PDB DOI: https://doi.org/10.2210/pdb1DQU/pdb

• Classification: LYASE
• Organism(s): Aspergillus nidulans
• Expression System: Aspergillus nidulans
• Mutation(s): No 


• Deposited: 2000-01-05 Released: 2000-05-10 
• Deposition Author(s): Britton, K.L., Langridge, S.J., Baker, P.J., Weeradechapon, K., Sedelnikova, S.E., De Lucas, J.R., Rice, D.W., Turner, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.376 
• R-Value Work: 0.273 
• R-Value Observed: 0.276 

Literature

The crystal structure and active site location of isocitrate lyase from the fungus Aspergillus nidulans.

Britton, K., Langridge, S., Baker, P.J., Weeradechapon, K., Sedelnikova, S.E., De Lucas, J.R., Rice, D.W., Turner, G.

(2000) Structure 8: 349-362

• PubMed: 10801489 
• DOI: https://doi.org/10.1016/s0969-2126(00)00117-9
• Primary Citation of Related Structures:  
  1DQU


• PubMed Abstract: 
  

  Isocitrate lyase catalyses the first committed step of the carbon-conserving glyoxylate bypass, the Mg(2+)-dependent reversible cleavage of isocitrate into succinate and glyoxylate. This metabolic pathway is an inviting target for the control of a number of diseases, because the enzymes involved in this cycle have been identified in many pathogens including Mycobacterium leprae and Leishmania.

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Organizational Affiliation: 

Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield, S10 2TN, UK.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 60.4 kDa 
• Atom Count: 4,069 
• Modelled Residue Count: 513 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ISOCITRATE LYASE	A	538	Aspergillus nidulans	Mutation(s): 0  EC: 4.1.3.1
UniProt
Find proteins for P28298 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)) Explore P28298  Go to UniProtKB:  P28298

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.376 
• R-Value Work: 0.273 
• R-Value Observed: 0.276 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.93	α = 90
b = 91.93	β = 90
c = 152.77	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
TNT	refinement
MOSFLM	data reduction
CCP4	data scaling
ROTAVATA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-05-10 
Deposition Author(s): Britton, K.L., Langridge, S.J., Baker, P.J., Weeradechapon, K., Sedelnikova, S.E., De Lucas, J.R., Rice, D.W., Turner, G.

Revision History  

• Version 1.0: 2000-05-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Advisory, Refinement description
• Version 1.4: 2024-02-07
  Changes: Advisory, Data collection, Database references