7LLQ

Substrate-dependent divergence of leukotriene A4 hydrolase aminopeptidase activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Substrate-dependent modulation of the leukotriene A 4 hydrolase aminopeptidase activity and effect in a murine model of acute lung inflammation.

Lee, K.H.Ali, N.F.Lee, S.H.Zhang, Z.Burdick, M.Beaulac, Z.J.Petruncio, G.Li, L.Xiang, J.Chung, E.M.Foreman, K.W.Noble, S.M.Shim, Y.M.Paige, M.

(2022) Sci Rep 12: 9443-9443

  • DOI: https://doi.org/10.1038/s41598-022-13238-6
  • Primary Citation of Related Structures:  
    7KZE, 7LLQ

  • PubMed Abstract: 

    The aminopeptidase activity (AP) of the leukotriene A 4 hydrolase (LTA 4 H) enzyme has emerged as a therapeutic target to modulate host immunity. Initial reports focused on the benefits of augmenting the LTA 4 H AP activity and clearing its putative pro-inflammatory substrate Pro-Gly-Pro (PGP). However, recent reports have introduced substantial complexity disconnecting the LTA 4 H modulator 4-methoxydiphenylmethane (4MDM) from PGP as follows: (1) 4MDM inhibits PGP hydrolysis and subsequently inhibition of LTA 4 H AP activity, and (2) 4MDM activates the same enzyme target in the presence of alternative substrates. Differential modulation of LTA 4 H by 4MDM was probed in a murine model of acute lung inflammation, which showed that 4MDM modulates the host neutrophilic response independent of clearing PGP. X-ray crystallography showed that 4MDM and PGP bind at the zinc binding pocket and no allosteric binding was observed. We then determined that 4MDM modulation is not dependent on the allosteric binding of the ligand, but on the N-terminal side chain of the peptide. In conclusion, our study revealed that a peptidase therapeutic target can interact with its substrate and ligand in complex biochemical mechanisms. This raises an important consideration when ligands are designed to explain some of the unpredictable outcomes observed in therapeutic discovery targeting LTA 4 H.


  • Organizational Affiliation

    Department of Chemistry & Biochemistry, George Mason University, 10920 George Mason Circle, Manassas, VA, 20110, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leukotriene A-4 hydrolase
A, B, C
611Homo sapiensMutation(s): 0 
Gene Names: LTA4HLTA4
EC: 3.3.2.6 (PDB Primary Data), 3.4.11.4 (PDB Primary Data)
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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
28T (Subject of Investigation/LOI)
Query on 28T

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C]
1-{4-oxo-4-[(2S)-pyrrolidin-2-yl]butanoyl}-L-proline
C13 H20 N2 O4
FCVBOVVXXBUFFZ-UWVGGRQHSA-N
N0Y (Subject of Investigation/LOI)
Query on N0Y

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C]
1-benzyl-4-methoxybenzene
C14 H14 O
GQLYCRTUQGSDSM-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
J [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.054α = 90
b = 138.054β = 90
c = 84.257γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
PROTEUMdata reduction
PROTEUMdata scaling
PROTEUMphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01HL132287

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description