1IGW

Crystal Structure of the Isocitrate Lyase from the A219C mutant of Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structure and domain organization of Escherichia coli isocitrate lyase.

Britton, K.L.Abeysinghe, I.S.Baker, P.J.Barynin, V.Diehl, P.Langridge, S.J.McFadden, B.A.Sedelnikova, S.E.Stillman, T.J.Weeradechapon, K.Rice, D.W.

(2001) Acta Crystallogr.,Sect.D 57: 1209-1218


  • PubMed Abstract: 
  • Enzymes of the glyoxylate-bypass pathway are potential targets for the control of many human diseases caused by such pathogens as Mycobacteria and Leishmania. Isocitrate lyase catalyses the first committed step in this pathway and the structure of th ...

    Enzymes of the glyoxylate-bypass pathway are potential targets for the control of many human diseases caused by such pathogens as Mycobacteria and Leishmania. Isocitrate lyase catalyses the first committed step in this pathway and the structure of this tetrameric enzyme from Escherichia coli has been determined at 2.1 A resolution. E. coli isocitrate lyase, like the enzyme from other prokaryotes, is located in the cytoplasm, whereas in plants, protozoa, algae and fungi this enzyme is found localized in glyoxysomes. Comparison of the structure of the prokaryotic isocitrate lyase with that from the eukaryote Aspergillus nidulans reveals a different domain structure following the deletion of approximately 100 residues from the larger eukaryotic enzyme. Despite this, the active sites of the prokaryotic and eukaryotic enzymes are very closely related, including the apparent disorder of two equivalent segments of the protein that are known to be involved in a conformational change as part of the enzyme's catalytic cycle.


    Related Citations: 
    • Use of Chemical Modification in the Crystallization of Isocitrate Lyase from Escherichia coli
      Abeysinghe, S.I.,Baker, P.J.,Rice, D.W.,Rodgers, H.F.,Stillman, T.J.,Ko, Y.H.,McFadden, B.A.,Nimmo, H.G.
      (1991) J.Mol.Biol. 220: 13


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Isocitrate lyase
A, B, C, D
434Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: aceA (icl)
EC: 4.1.3.1
Find proteins for P0A9G6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A9G6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PYR
Query on PYR

Download SDF File 
Download CCD File 
A, B, C, D
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HG
Query on HG

Download SDF File 
Download CCD File 
A, B, C, D
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.184 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 88.650α = 90.00
b = 88.650β = 90.00
c = 199.400γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
CCP4phasing
TFFCmodel building
DMmodel building
DMphasing
ROTAVATAdata scaling
TFFCphasing
MOSFLMdata reduction
CCP4data scaling
CCP4model building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-09-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description