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 
  • R-Value Observed: 0.160 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1073/pnas.1710850114
  • Primary Citation of Related Structures:  
    4DPR, 5NI2, 5NI4, 5NI6, 5NIA, 5NID, 5NIE

  • PubMed Abstract: 

    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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leukotriene A-4 hydrolase617Homo sapiensMutation(s): 1 
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
GTEx:  ENSG00000111144 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09960
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DJ3
Query on DJ3

Download Ideal Coordinates CCD File 
F [auth A]5S-5,6-oxido-7,9-trans-11,14-cis-eicosatetraenoic acid
C20 H30 O3
UFPQIRYSPUYQHK-WAQVJNLQSA-N
YB
Query on YB

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

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

Download Ideal Coordinates CCD File 
E [auth A],
G [auth A]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.13α = 90
b = 87.45β = 90
c = 99.46γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sweden--

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description