1MUM

Structure of the 2-Methylisocitrate Lyase (PrpB) from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of 2-methylisocitrate lyase (PrpB) from Escherichia coli and modelling of its ligand bound active centre.

Grimm, C.Evers, A.Brock, M.Maerker, C.Klebe, G.Buckel, W.Reuter, K.

(2003) J.Mol.Biol. 328: 609-621


  • PubMed Abstract: 
  • Following acetate, propionate is the second most abundant low molecular mass carbon compound found in soil. Many microorganisms, including most, if not all fungi, as well as several aerobic bacteria, such as Escherichia coli and Salmonella enterica o ...

    Following acetate, propionate is the second most abundant low molecular mass carbon compound found in soil. Many microorganisms, including most, if not all fungi, as well as several aerobic bacteria, such as Escherichia coli and Salmonella enterica oxidize propionate via the methylcitrate cycle. The enzyme 2-methylisocitrate lyase (PrpB) from Escherichia coli catalysing the last step of this cycle, the cleavage of 2-methylisocitrate to pyruvate and succinate, was crystallised and its structure determined to a resolution of 1.9A. The enzyme, which strictly depends on Mg(2+) for catalysis, belongs to the isocitrate lyase protein family. A common feature of members of this enzyme family is the movement of a so-called "active site loop" from an open into a closed conformation upon substrate binding thus shielding the reactants from the surrounding solvent. Since in the presented structure, PrpB contains, apart from a Mg(2+), no ligand, the active site loop is found in an open conformation. This conformation, however, differs significantly from the open conformation present in the so far known structures of ligand-free isocitrate lyases. A possible impact of this observation with respect to the different responses of isocitrate lyases and PrpB upon treatment with the common inhibitor 3-bromopyruvate is discussed. Based on the structure of ligand-bound isocitrate lyase from Mycobacterium tuberculosis a model of the substrate-bound PrpB enzyme in its closed conformation was created which provides hints towards the substrate specificity of this enzyme.


    Organizational Affiliation

    Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-methylisocitrate lyase
A, B
295Escherichia coli (strain K12)Gene Names: prpB (yahQ)
EC: 4.1.3.30
Find proteins for P77541 (Escherichia coli (strain K12))
Go to UniProtKB:  P77541
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.213 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 82.895α = 90.00
b = 82.895β = 90.00
c = 166.250γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2002-09-24 
  • Released Date: 2003-04-29 
  • Deposition Author(s): Grimm, C., Reuter, K.

Revision History 

  • Version 1.0: 2003-04-29
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description