7DLS | pdb_00007dls

Cytochrome P450 (CYP105D18) complex with papaverine

• PDB DOI: https://doi.org/10.2210/pdb7DLS/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces laurentii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-11-30 Released: 2021-07-14 
• Deposition Author(s): Do, H., Lee, J.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.218 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.172 (Depositor) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

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

• PubMed: 34258016 
• DOI: https://doi.org/10.1107/S2052252521005522
• Primary Citation 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.
Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea.
Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea.
Genome-based BioIT Convergence Institute, Asan 31460, Republic of Korea.
Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan 31460, Republic of Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 45.36 kDa 
• Atom Count: 3,223 
• Modeled Residue Count: 392 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 hydroxylase	A	396	Streptomyces laurentii	Mutation(s): 0  Gene Names: SLA_5925
UniProt
Find proteins for A0A160P685 (Streptomyces laurentii) Explore A0A160P685  Go to UniProtKB:  A0A160P685

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
EV1 (Subject of Investigation/LOI)	C [auth A]	1-(3,4-DIMETHOXYBENZYL)-6,7-DIMETHOXYISOQUINOLINE C20 H21 N O4 XQYZDYMELSJDRZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.218 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.172 (Depositor) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.522	α = 90
b = 52.172	β = 110.68
c = 87.896	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): Do, H., Lee, J.H.

Revision History  

• 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, Structure summary