7DI3

Cytochrome P450 (CYP105D18) W.T.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Characterization of high-H 2 O 2 -tolerant bacterial cytochrome P450 CYP105D18: insights into papaverine N-oxidation.

Pardhe, B.D.Do, H.Jeong, C.S.Kim, K.H.Lee, J.H.Oh, T.J.

(2021) IUCrJ 8: 684-694

  • DOI: https://doi.org/10.1107/S2052252521005522
  • Primary Citation of Related Structures:  
    7DI3, 7DLS

  • PubMed Abstract: 

    The bacterial CYP105 family is involved in secondary metabolite biosynthetic pathways and plays essential roles in the biotransformation of xenobiotics. This study investigates the newly identified H 2 O 2 -mediated CYP105D18 from Streptomyces laurentii as the first bacterial CYP for N-oxidation. The catalytic efficiency of CYP105D18 for papaverine N-oxidation was 1.43 s -1  µ M -1 . The heme oxidation rate ( k ) was low (<0.3 min -1 ) in the presence of 200 m M H 2 O 2 . This high H 2 O 2 tolerance capacity of CYP105D18 led to higher turnover prior to heme oxidation. Additionally, the high-resolution papaverine complexed structure and substrate-free structure of CYP105D18 were determined. Structural analysis and activity assay results revealed that CYP105D18 had a strong substrate preference for papaverine because of its bendable structure. These findings establish a basis for biotechnological applications of CYP105D18 in the pharmaceutical and medicinal industries.


  • Organizational Affiliation

    Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan 31460, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450 hydroxylase396Streptomyces laurentiiMutation(s): 0 
Gene Names: SLA_5925
UniProt
Find proteins for A0A160P685 (Streptomyces laurentii)
Explore A0A160P685 
Go to UniProtKB:  A0A160P685
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A160P685
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.688α = 90
b = 52.444β = 110.82
c = 87.952γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description