5NI6

Crystal structure of human LTA4H mutant D375N in complex with LTA4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Capturing LTA4 hydrolase in action: Insights to the chemistry and dynamics of chemotactic LTB4 synthesis.

Stsiapanava, A.Samuelsson, B.Haeggstrom, J.Z.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 9689-9694

  • DOI: 10.1073/pnas.1710850114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human leukotriene (LT) A4 hydrolase/aminopeptidase (LTA4H) is a bifunctional enzyme that converts the highly unstable epoxide intermediate LTA4 into LTB4, a potent leukocyte activating agent, while the aminopeptidase activity cleaves and inactivates ...

    Human leukotriene (LT) A4 hydrolase/aminopeptidase (LTA4H) is a bifunctional enzyme that converts the highly unstable epoxide intermediate LTA4 into LTB4, a potent leukocyte activating agent, while the aminopeptidase activity cleaves and inactivates the chemotactic tripeptide Pro-Gly-Pro. Here, we describe high-resolution crystal structures of LTA4H complexed with LTA4, providing the structural underpinnings of the enzyme's unique epoxide hydrolase (EH) activity, involving Zn2+, Y383, E271, D375, and two catalytic waters. The structures reveal that a single catalytic water is involved in both catalytic activities of LTA4H, alternating between epoxide ring opening and peptide bond hydrolysis, assisted by E271 and E296, respectively. Moreover, we have found two conformations of LTA4H, uncovering significant domain movements. The resulting structural alterations indicate that LTA4 entrance into the active site is a dynamic process that includes rearrangement of three moving domains to provide fast and efficient alignment and processing of the substrate. Thus, the movement of one dynamic domain widens the active site entrance, while another domain acts like a lid, opening and closing access to the hydrophobic tunnel, which accommodates the aliphatic tale of LTA4 during EH reaction. The enzyme-LTA4 complex structures and dynamic domain movements provide critical insights for development of drugs targeting LTA4H.


    Organizational Affiliation

    Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Leukotriene A-4 hydrolase
A
617Homo 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
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DJ3
Query on DJ3

Download SDF File 
Download CCD File 
A
5S-5,6-oxido-7,9-trans-11,14-cis-eicosatetraenoic acid
C20 H30 O3
UFPQIRYSPUYQHK-WAQVJNLQSA-N
 Ligand Interaction
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
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: 1.54 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.130α = 90.00
b = 87.450β = 90.00
c = 99.460γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-03-23 
  • Released Date: 2017-08-23 
  • Deposition Author(s): Stsiapanava, A.

Funding OrganizationLocationGrant Number
Sweden--

Revision History 

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Database references