7LES

Acanthamoeba castellanii CYP51 (AcCYP51)-Imidazole complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Homodimerization Counteracts the Detrimental Effect of Nitrogenous Heme Ligands on the Enzymatic Activity of Acanthamoeba castellanii CYP51.

Nienhaus, K.Sharma, V.Nienhaus, G.U.Podust, L.M.

(2022) Biochemistry 61: 1363-1377

  • DOI: https://doi.org/10.1021/acs.biochem.2c00198
  • Primary Citation of Related Structures:  
    7LES

  • PubMed Abstract: 

    Acanthamoeba castellanii is a free-living amoeba that can cause severe eye and brain infections in humans. At present, there is no uniformly effective treatment for any of these infections. However, sterol 14α-demethylases (CYP51s), heme-containing cytochrome P450 enzymes, are known to be validated drug targets in pathogenic fungi and protozoa. The catalytically active P450 form of CYP51 from A. castellanii (AcCYP51) is stabilized against conversion to the inactive P420 form by dimerization. In contrast, Naegleria fowleri CYP51 (NfCYP51) is monomeric in its active P450 and inactive P420 forms. For these two CYP51 enzymes, we have investigated the interplay between the enzyme activity and oligomerization state using steady-state and time-resolved UV-visible absorption spectroscopy. In both enzymes, the P450 → P420 transition is favored under reducing conditions. The transition is accelerated at higher pH, which excludes a protonated thiol as the proximal ligand in P420. Displacement of the proximal thiolate ligand is also promoted by adding exogenous nitrogenous ligands (N-ligands) such as imidazole, isavuconazole, and clotrimazole that bind at the opposite, distal heme side. In AcCYP51, the P450 → P420 transition is faster in the monomer than in the dimer, indicating that the dimeric assembly is critical for stabilizing thiolate coordination to the heme and thus for sustaining AcCYP51 activity. The spectroscopic experiments were complemented with size-exclusion chromatography and X-ray crystallography studies. Collectively, our results indicate that effective inactivation of the AcCYP51 function by azole drugs is due to synergistic interference with AcCYP51 dimerization and promoting irreversible displacement of the proximal heme-thiolate ligand.


  • Organizational Affiliation

    Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), D-76049 Karlsruhe, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Obtusifoliol 14alphademethylase, putative
A, B, C, D
460Acanthamoeba castellanii str. NeffMutation(s): 0 
Gene Names: ACA1_372720
UniProt
Find proteins for L8GJB3 (Acanthamoeba castellanii (strain ATCC 30010 / Neff))
Explore L8GJB3 
Go to UniProtKB:  L8GJB3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL8GJB3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
N [auth C],
R [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A]
I [auth B]
K [auth B]
Q [auth D]
S [auth D]
F [auth A],
I [auth B],
K [auth B],
Q [auth D],
S [auth D],
U [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
IMD (Subject of Investigation/LOI)
Query on IMD

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
O [auth C],
T [auth D]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
FMT
Query on FMT

Download Ideal Coordinates CCD File 
H [auth A],
M [auth B],
P [auth C]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.56α = 90
b = 125.58β = 90.04
c = 100.51γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-22
    Type: Initial release
  • Version 1.1: 2022-07-06
    Changes: Database references, Derived calculations
  • Version 1.2: 2022-07-20
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description