3B7S

[E296Q]LTA4H in complex with RSR substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.465 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.128 

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: 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
    • 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
    • Assay for rapid analysis of the tri-peptidase activity of LTA4 hydrolase.
      Tholander, F.,Haeggstrom, J.Z.
      (2007) Proteins 67: 1113
    • 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


    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
A
616Homo sapiensMutation(s): 1 
Gene Names: LTA4H (LTA4)
EC: 3.3.2.6
Find proteins for P09960 (Homo sapiens)
Go to Gene View: LTA4H
Go to UniProtKB:  P09960
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RSR peptide
B
3N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 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
YB
Query on YB

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

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.465 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.128 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.508α = 90.00
b = 87.351β = 90.00
c = 99.769γ = 90.00
Software Package:
Software NamePurpose
SHELXrefinement
XFITdata reduction
SCALAdata scaling
SHELXL-97refinement
MOSFLMdata reduction
PDB_EXTRACTdata extraction

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: Non-polymer description, Version format compliance
  • Version 1.2: 2018-03-07
    Type: Advisory, Data collection