4DPR

Structure of human Leukotriene A4 hydrolase in complex with inhibitor captopril


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Capturing LTA4hydrolase in action: Insights to the chemistry and dynamics of chemotactic LTB4synthesis.

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) A <sub>4 </sub> hydrolase/aminopeptidase (LTA <sub>4 </sub>H) is a bifunctional enzyme that converts the highly unstable epoxide intermediate LTA <sub>4 </sub> into LTB <sub>4 </sub>, a potent leukocyte activating agent, while ...

    Human leukotriene (LT) A 4 hydrolase/aminopeptidase (LTA 4 H) is a bifunctional enzyme that converts the highly unstable epoxide intermediate LTA 4 into LTB 4 , 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 LTA 4 H complexed with LTA 4 , providing the structural underpinnings of the enzyme's unique epoxide hydrolase (EH) activity, involving Zn 2+ , Y383, E271, D375, and two catalytic waters. The structures reveal that a single catalytic water is involved in both catalytic activities of LTA 4 H, alternating between epoxide ring opening and peptide bond hydrolysis, assisted by E271 and E296, respectively. Moreover, we have found two conformations of LTA 4 H, uncovering significant domain movements. The resulting structural alterations indicate that LTA 4 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 LTA 4 during EH reaction. The enzyme-LTA 4 complex structures and dynamic domain movements provide critical insights for development of drugs targeting LTA 4 H.


    Organizational Affiliation

    Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden bengt.samuelsson@ki.se jesper.haeggstrom@ki.se.,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
611Homo 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 5 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
X8Z
Query on X8Z

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Download CCD File 
A
L-CAPTOPRIL
C9 H15 N O3 S
FAKRSMQSSFJEIM-RQJHMYQMSA-N
 Ligand Interaction
YB
Query on YB

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

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

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Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
X8ZIC50: 70 - 630000 nM (100) BINDINGDB
X8ZKi: 3700 nM (100) BINDINGDB
X8ZKd: 6250 - 8470 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 77.552α = 90.00
b = 87.398β = 90.00
c = 99.592γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MAR345data collection
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2017-08-23
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description
  • Version 1.3: 2018-04-25
    Type: Data collection, Database references