7WEX

The crystal structure of substrate-free CYP107X1 from Streptomyces avermitilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

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Literature

The 16 alpha-Hydroxylation of Progesterone by Cytochrome P450 107X1 from Streptomyces avermitilis.

Lin, S.Ma, B.Gao, Q.Yang, J.Lai, G.Lin, R.Yang, B.Han, B.N.Xu, L.H.

(2022) Chem Biodivers 19: e202200177-e202200177

  • DOI: https://doi.org/10.1002/cbdv.202200177
  • Primary Citation of Related Structures:  
    7WEX

  • PubMed Abstract: 

    Cytochrome P450 enzymes (CYPs or P450s) are ubiquitous heme-dependent enzymes that catalyze the monooxygenation of non-activated C-H bonds to modify the structure of the substrate. In this study, we heterologously expressed CYP107X1 from Streptomyces avermitilis and conducted in vitro substrate screening using the alternative redox partners putidaredoxin and putidaredoxin reductase. CYP107X1 catalyzed the 16α-hydroxylation of progesterone with regio- and stereoselectivity. The spectroscopic analyses showed that CYP107X1 bound progesterone with a relatively high K d value of 65.3±38.9 μM. The K m and k cat values for progesterone were estimated to be 47.7±12.0 μM and 0.30 min -1 , respectively. Furthermore, a crystal structure was obtained of CYP107X1 bound with glycerol from the buffer solution. Interestingly, a conserved threonine was replaced with asparagine in CYP107X1, indicating that it may adopt an unnatural proton transfer process and play a crucial role in its catalytic activity.


  • Organizational Affiliation

    College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450 hydroxylase408Streptomyces avermitilis MA-4680 = NBRC 14893Mutation(s): 0 
Gene Names: cyp23SAVERM_6249
UniProt
Find proteins for Q82A10 (Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680))
Explore Q82A10 
Go to UniProtKB:  Q82A10
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ82A10
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.381α = 90
b = 83.381β = 90
c = 93.805γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

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)81402810

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-29
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description