2R59

Leukotriene A4 hydrolase complexed with inhibitor RB3041


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    2R59, 3B7R, 3B7S, 3B7T, 3B7U

  • 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 coordinating groups, while maintaining the overall coordination geometry ...

    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: 
    • Assay for rapid analysis of the tri-peptidase activity of LTA4 hydrolase.
      Tholander, F., Haeggstrom, J.Z.
      (2007) Proteins 67: 1113
    • 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
    • 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
    • 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 U S A 99: 4215
    • Crystal structure of human leukotriene A(4) hydrolase, a bifunctional enzyme in inflammation.
      Thunnissen, M.M., Nordlund, P., Haeggstrom, J.Z.
      (2001) Nat Struct Biol 8: 131

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Leukotriene A-4 hydrolaseA616Homo sapiensMutation(s): 0 
Gene Names: LTA4HLTA4
EC: 3.3.2.6 (PDB Primary Data), 3.4.11.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P09960 (Homo sapiens)
Explore P09960 
Go to UniProtKB:  P09960
PHAROS:  P09960
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PH0
Query on PH0

Download Ideal Coordinates CCD File 
D [auth A]N-{(2S)-3-[(R)-[(1R)-1-amino-2-phenylethyl](hydroxy)phosphoryl]-2-benzylpropanoyl}-L-phenylalanine
C27 H31 N2 O5 P
XNPYGVCNHOXQRJ-DSNGMDLFSA-N
 Ligand Interaction
YB
Query on YB

Download Ideal Coordinates CCD File 
C [auth A]YTTERBIUM (III) ION
Yb
AWSFICBXMUKWSK-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download Ideal Coordinates CCD File 
E [auth A]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PH0Ki:  6.5   nM  Binding MOAD
PH0Ki :  6.5   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.21α = 90
b = 87.23β = 90
c = 99.23γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XSCALEdata scaling
XFITdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-03-07
    Changes: Data collection
  • Version 1.3: 2019-11-20
    Changes: Database references, Derived calculations