3B7R

Leukotriene A4 Hydrolase Complexed with Inhibitor RB3040


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.811 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-based dissection of the active site chemistry of leukotriene a4 hydrolase: implications for m1 aminopeptidases and inhibitor design.

Tholander, F.Muroya, A.Roques, B.P.Fournie-Zaluski, M.C.Thunnissen, M.M.Haeggstrom, J.Z.

(2008) Chem.Biol. 15: 920-929

  • DOI: 10.1016/j.chembiol.2008.07.018
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • M1 aminopeptidases comprise a large family of biologically important zinc enzymes. We show that peptide turnover by the M1 prototype, leukotriene A4 hydrolase/aminopeptidase, involves a shift in substrate position associated with exchange of zinc coo ...

    M1 aminopeptidases comprise a large family of biologically important zinc enzymes. We show that peptide turnover by the M1 prototype, leukotriene A4 hydrolase/aminopeptidase, involves a shift in substrate position associated with exchange of zinc coordinating groups, while maintaining the overall coordination geometry. The transition state is stabilized by residues conserved among M1 members and in the final reaction step, Glu-296 of the canonical zinc binding HEXXH motif shuffles a proton from the hydrolytic water to the leaving group. Tripeptide substrates bind along the conserved GXMEN motif, precisely occupying the distance between Glu-271 and Arg-563, whereas the Arg specificity is governed by a narrow S1 pocket capped with Asp-375. Our data provide detailed insights to the active site chemistry of M1 aminopeptidases and will aid in the development of novel enzyme inhibitors.


    Related Citations: 
    • Leukotriene A4 hydrolase/aminopeptidase. Glutamate 271 is a catalytic residue with specific roles in two distinct enzyme mechanisms.
      Rudberg, P.C.,Tholander, F.,Thunnissen, M.M.,Haeggstrom, J.Z.
      (2002) J.Biol.Chem. 277: 1398
    • Assay for rapid analysis of the tri-peptidase activity of LTA4 hydrolase.
      Tholander, F.,Haeggstrom, J.Z.
      (2007) Proteins 67: 1113
    • Crystal structure of human leukotriene A(4) hydrolase, a bifunctional enzyme in inflammation.
      Thunnissen, M.M.,Nordlund, P.,Haeggstrom, J.Z.
      (2001) Nat.Struct.Mol.Biol. 8: 131
    • Leukotriene A4 hydrolase: selective abrogation of leukotriene B4 formation by mutation of aspartic acid 375.
      Rudberg, P.C.,Tholander, F.,Thunnissen, M.M.,Samuelsson, B.,Haeggstrom, J.Z.
      (2002) Proc.Natl.Acad.Sci.USA 99: 4215
    • Leukotriene A4 hydrolase: identification of a common carboxylate recognition site for the epoxide hydrolase and aminopeptidase substrates.
      Rudberg, P.C.,Tholander, F.,Andberg, M.,Thunnissen, M.M.,Haeggstrom, J.Z.
      (2004) J.Biol.Chem. 279: 27376


    Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Division of Chemistry II, Karolinska Institute, Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Leukotriene A-4 hydrolase
L
616Homo sapiensMutation(s): 0 
Gene Names: LTA4H (LTA4)
EC: 3.3.2.6
Find proteins for P09960 (Homo sapiens)
Go to Gene View: LTA4H
Go to UniProtKB:  P09960
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
YB
Query on YB

Download SDF File 
Download CCD File 
L
YTTERBIUM (III) ION
Yb
AWSFICBXMUKWSK-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

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Download CCD File 
L
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
BIR
Query on BIR

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Download CCD File 
L
N-[3-[(1-AMINOETHYL)(HYDROXY)PHOSPHORYL]-2-(1,1'-BIPHENYL-4-YLMETHYL)PROPANOYL]ALANINE
C21 H27 N2 O5 P
CWJPVKSBGVPXRD-QMTMVMCOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BIRKi: 20 nM BINDINGMOAD
BIRKi: 20 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.811 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.149 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.330α = 90.00
b = 86.937β = 90.00
c = 99.109γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2018-03-07
    Type: Data collection