6A7I

CYP154C4 from Streptomyces sp. W2061


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Characterization of two steroid hydroxylases from different Streptomyces spp. and their ligand-bound and -unbound crystal structures.

Dangi, B.Lee, C.W.Kim, K.H.Park, S.H.Yu, E.J.Jeong, C.S.Park, H.Lee, J.H.Oh, T.J.

(2019) Febs J. 286: 1683-1699

  • DOI: 10.1111/febs.14729
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial cytochrome P450 (CYP) enzymes are involved in the hydroxylation of various endogenous substrates while using a heme molecule as a cofactor. CYPs have gained biotechnological interest as useful biocatalysts capable of altering chemical struc ...

    Bacterial cytochrome P450 (CYP) enzymes are involved in the hydroxylation of various endogenous substrates while using a heme molecule as a cofactor. CYPs have gained biotechnological interest as useful biocatalysts capable of altering chemical structures by adding a hydroxyl group in a regiospecific manner. Here, we identified, purified, and characterized two CYP154C4 proteins from Streptomyces sp. W2061 (StCYP154C4-1) and Streptomyces sp. ATCC 11861 (StCYP154C4-2). Activity assays showed that both StCYP154C4-1 and StCYP154C4-2 can produce 2'-hydroxylated testosterone, which differs from the activity of a previously described NfCYP154C5 from Nocardia farcinica in terms of its 16α-hydroxylation of testosterone. To better understand the molecular basis of the regioselectivity of these two CYP154C4 proteins, crystal structures of the ligand-unbound form of StCYP154C4-1 and the testosterone-bound form of StCYP154C4-2 were determined. Comparison with the previously determined NfCYP154C5 structure revealed differences in the substrate-binding residues, suggesting a likely explanation for the different patterns of testosterone hydroxylation, despite the high sequence similarities between the enzymes (54% identity). These findings provide valuable insights that will enable protein engineering for the development of artificial steroid-related CYPs exhibiting different regiospecificity.


    Organizational Affiliation

    Department of Polar Sciences, University of Science and Technology, Incheon, Korea.,Department of Pharmaceutical Engineering and Biotechnology, Sunmoon University, Asansi, Korea.,Department of Life Science and Biochemical Engineering, Sunmoon University, Asansi, Korea.,Genome-based BioIT Convergence Institute, Asansi, Korea.,Unit of Polar Genomics, Korea Polar Research Institute, Incheon, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450
A
411Streptomyces sp. JS01Mutation(s): 0 
Find proteins for A0A087KD84 (Streptomyces sp. JS01)
Go to UniProtKB:  A0A087KD84
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.173 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 83.755α = 90.00
b = 115.032β = 90.00
c = 127.807γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
MxDCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-07-03 
  • Released Date: 2019-01-16 
  • Deposition Author(s): Lee, C.W., Lee, J.H.

Revision History 

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-05-22
    Type: Data collection, Database references