7CL8

Testosterone-bound structure of CYP154C2 from Streptomyces avermitilis in an closed conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Improved 2 alpha-Hydroxylation Efficiency of Steroids by CYP154C2 Using Structure-Guided Rational Design.

Gao, Q.Ma, B.Wang, Q.Zhang, H.Fushinobu, S.Yang, J.Lin, S.Sun, K.Han, B.N.Xu, L.H.

(2023) Appl Environ Microbiol 89: e0218622-e0218622

  • DOI: https://doi.org/10.1128/aem.02186-22
  • Primary Citation of Related Structures:  
    7CL8

  • PubMed Abstract: 

    Cytochrome P450 enzymes are promising biocatalysts for industrial use because they catalyze site-selective C-H oxidation and have diverse catalytic reactions and a broad substrate range. In this study, the 2α-hydroxylation activity of CYP154C2 from Streptomyces avermitilis MA-4680T toward androstenedione (ASD) was identified by an in vitro conversion assay. The testosterone (TES)-bound structure of CYP154C2 was solved at 1.42 Å, and this structure was used to design eight mutants, including single, double, and triple mutants, to improve the conversion efficiency. Mutants L88F/M191F and M191F/V285L were found to enhance the conversion rates significantly (i.e., 8.9-fold and 7.4-fold for TES, 46.5-fold and 19.5-fold for ASD, respectively) compared with the wild-type (WT) enzyme while retaining high 2α-position selectivity. The substrate binding affinity of the L88F/M191F mutant toward TES and ASD was enhanced compared with that of WT CYP154C2, supporting the measured increase in the conversion efficiencies. Moreover, the total turnover number and k cat / K m of the L88F/M191F and M191F/V285L mutants increased significantly. Interestingly, all mutants containing L88F generated 16α-hydroxylation products, suggesting that L88 in CYP154C2 plays a vital role in substrate selectivity and that the amino acid corresponding to L88 in the 154C subfamily affects the orientation of steroid binding and substrate selectivity. IMPORTANCE Hydroxylated derivatives of steroids play essential roles in medicine. Cytochrome P450 enzymes selectively hydroxylate methyne groups on steroids, which can dramatically change their polarity, biological activity and toxicity. There is a paucity of reports on the 2α-hydroxylation of steroids, and documented 2α-hydroxylate P450s show extremely low conversion efficiency and/or low regio- and stereoselectivity. This study conducted crystal structure analysis and structure-guided rational engineering of CYP154C2 and efficiently enhanced the conversion efficiency of TES and ASD with high regio- and stereoselectivity. Our results provide an effective strategy and theoretical basis for the 2α-hydroxylation of steroids, and the structure-guided rational design of P450s should facilitate P450 applications in the biosynthesis of steroid drugs.


  • Organizational Affiliation

    College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450 hydroxylase420Streptomyces avermitilis MA-4680 = NBRC 14893Mutation(s): 0 
Gene Names: cyp19SAVERM_3882
UniProt
Find proteins for Q82GL5 (Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680))
Explore Q82GL5 
Go to UniProtKB:  Q82GL5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ82GL5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

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

Download Ideal Coordinates CCD File 
F [auth A]TESTOSTERONE
C19 H28 O2
MUMGGOZAMZWBJJ-DYKIIFRCSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
C [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.74α = 90
b = 61.82β = 90
c = 133.77γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81402810

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description