2XQ0

Structure of yeast LTA4 hydrolase in complex with Bestatin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.955 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A Leukotriene A(4) Hydrolase-Related Aminopeptidase from Yeast Undergoes Induced Fit Upon Inhibitor Binding.

Helgstrand, C.Hasan, M.Usyal, H.Haeggstrom, J.Z.Thunnissen, M.M.G.M.

(2011) J.Mol.Biol. 406: 120

  • DOI: 10.1016/j.jmb.2010.11.059
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Vertebrate leukotriene A(4) hydrolases are bifunctional zinc metalloenzymes with an epoxide hydrolase and an aminopeptidase activity. In contrast, highly homologous enzymes from lower organisms only have the aminopeptidase activity. From sequence com ...

    Vertebrate leukotriene A(4) hydrolases are bifunctional zinc metalloenzymes with an epoxide hydrolase and an aminopeptidase activity. In contrast, highly homologous enzymes from lower organisms only have the aminopeptidase activity. From sequence comparisons, it is not clear why this difference occurs. In order to obtain more information on the evolutionary relationship between these enzymes and their activities, the structure of a closely related leucine aminopeptidase from Saccharomyces cerevisiae that only shows a very low epoxide hydrolase activity was determined. To investigate the molecular architecture of the active site, the structures of both the native protein and the protein in complex with the aminopeptidase inhibitor bestatin were solved. These structures show a more spacious active site, and the protected cavity in which the labile substrate leukotriene A(4) is bound in the human enzyme is partially obstructed and in other parts is more solvent accessible. Furthermore, the enzyme undergoes induced fit upon binding of the inhibitor bestatin, leading to a movement of the C-terminal domain. The main triggers for the domain movement are a conformational change of Tyr312 and a subtle change in backbone conformation of the PYGAMEN fingerprint region for peptide substrate recognition. This leads to a change in the hydrogen-bonding network pulling the C-terminal domain into a different position. Inasmuch as bestatin is a structural analogue of a leucyl dipeptide and may be regarded as a transition state mimic, our results imply that the enzyme undergoes induced fit during substrate binding and turnover.


    Organizational Affiliation

    Centre of Molecular Protein Science, Lund University, Getingev├Ągen 60, SE 22100 Lund, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LEUKOTRIENE A-4 HYDROLASE
A
632Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: LAP2
EC: 3.3.2.6
Find proteins for Q10740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q10740
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BES
Query on BES

Download SDF File 
Download CCD File 
A
2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID
BESTATIN
C16 H24 N2 O4
VGGGPCQERPFHOB-RDBSUJKOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.955 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.641α = 90.00
b = 99.874β = 90.00
c = 112.651γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-29
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-17
    Type: Data collection