6TO2

Crystal structure of CYP154C5 from Nocardia farcinica in complex with 5alpha-Androstan-3-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

CYP154C5 Regioselectivity in Steroid Hydroxylation Explored by Substrate Modifications and Protein Engineering*.

Bracco, P.Wijma, H.J.Nicolai, B.Buitrago, J.A.R.Klunemann, T.Vila, A.Schrepfer, P.Blankenfeldt, W.Janssen, D.B.Schallmey, A.

(2021) Chembiochem 22: 1099-1110

  • DOI: https://doi.org/10.1002/cbic.202000735
  • Primary Citation of Related Structures:  
    6TO2

  • PubMed Abstract: 

    CYP154C5 from Nocardia farcinica is a P450 monooxygenase able to hydroxylate a range of steroids with high regio- and stereoselectivity at the 16α-position. Using protein engineering and substrate modifications based on the crystal structure of CYP154C5, an altered regioselectivity of the enzyme in steroid hydroxylation had been achieved. Thus, conversion of progesterone by mutant CYP154C5 F92A resulted in formation of the corresponding 21-hydroxylated product 11-deoxycorticosterone in addition to 16α-hydroxylation. Using MD simulation, this altered regioselectivity appeared to result from an alternative binding mode of the steroid in the active site of mutant F92A. MD simulation further suggested that the entrance of water to the active site caused higher uncoupling in this mutant. Moreover, exclusive 15α-hydroxylation was observed for wild-type CYP154C5 in the conversion of 5α-androstan-3-one, lacking an oxy-functional group at C17. Overall, our data give valuable insight into the structure-function relationship of this cytochrome P450 monooxygenase for steroid hydroxylation.


  • Organizational Affiliation

    Biocatalysis, Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450 monooxygenase
A, B
409Nocardia farcinica IFM 10152Mutation(s): 0 
Gene Names: NFA_53110
UniProt
Find proteins for Q5YNS8 (Nocardia farcinica (strain IFM 10152))
Explore Q5YNS8 
Go to UniProtKB:  Q5YNS8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5YNS8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NQ8 (Subject of Investigation/LOI)
Query on NQ8

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
(5~{S},8~{S},9~{S},10~{S},13~{S},14~{S})-10,13-dimethyl-1,2,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydrocyclopenta[a]phenanthren-3-one
C19 H30 O
VMNRNUNYBVFVQI-QYXZOKGRSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.411α = 90
b = 103.411β = 90
c = 218.21γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing
DIALSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermany2223

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2021-03-31
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary