5IT1 | pdb_00005it1

Streptomyces peucetius CYP105P2 complex with biphenyl compound

• PDB DOI: https://doi.org/10.2210/pdb5IT1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces peucetius
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-03-16 Released: 2016-06-08 
• Deposition Author(s): Lee, C.W., Lee, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.243 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Crystal Structure of Cytochrome P450 (CYP105P2) from Streptomyces peucetius and Its Conformational Changes in Response to Substrate Binding

Lee, C.W., Lee, J.H., Rimal, H., Park, H., Lee, J.H., Oh, T.J.

(2016) Int J Mol Sci 17

• PubMed: 27231902 
• DOI: https://doi.org/10.3390/ijms17060813
• Primary Citation Related Structures: 
  5IT1


• PubMed Abstract: 
  

  Cytochrome P450 monooxygenases (CYP, EC 1.14.14.1) belong to a large family of enzymes that catalyze the hydroxylation of various substrates. Here, we present the crystal structure of CYP105P2 isolated from Streptomyces peucetius ATCC27952 at a 2.1 Å resolution. The structure shows the presence of a pseudo-ligand molecule in the active site, which was co-purified fortuitously and is presumed to be a biphenyl derivative. Comparison with previously determined substrate-bound CYP structures showed that binding of the ligand produces large and distinctive conformational changes in α2-α3, α7-α9, and the C-terminal loop regions. This structural flexibility confirms our previous observation that CYP105P2 can accommodate a broad range of ligands. The structure complexed with a pseudo-ligand provides the first molecular view of CYP105P2-ligand interactions, and it indicates the involvement of hydrophobic residues (Pro82, Ala181, Met187, Leu189, Leu193, and Ile236) in the interactions between hydrophobic ligands and CYP105P2. These results provide useful insights into the structural changes involved in the recognition of different ligands by CYP105P2.

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Organizational Affiliation: 
• Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Korea. [e-mail].
Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Korea. [e-mail].
Department of BT-Convergent Pharmaceutical Engineering, Sunmoon University, Asansi 336-708, Korea. [e-mail].
Department of BT-Convergent Pharmaceutical Engineering, Sunmoon University, Asansi 336-708, Korea. [e-mail].
Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Korea. [e-mail].
Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Korea. [e-mail].
Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Korea. [e-mail].
Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Korea. [e-mail].
Department of BT-Convergent Pharmaceutical Engineering, Sunmoon University, Asansi 336-708, Korea. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 178.16 kDa 
• Atom Count: 13,065 
• Modeled Residue Count: 1,580 
• Deposited Residue Count: 1,596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative cytochrome P450	A, B, C, D	399	Streptomyces peucetius	Mutation(s): 0  Gene Names: cyp7863 EC: 1.14.14.1
UniProt
Find proteins for Q70AS3 (Streptomyces peucetius) Explore Q70AS3  Go to UniProtKB:  Q70AS3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], G [auth B], I [auth C], K [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
2OH	F [auth A], H [auth B], J [auth C], L [auth D]	4,4'-PROPANE-2,2-DIYLDIPHENOL C15 H16 O2 IISBACLAFKSPIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.243 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.023	α = 90
b = 122.941	β = 90.028
c = 193.287	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-08 
Deposition Author(s): Lee, C.W., Lee, J.H.

Revision History  

• Version 1.0: 2016-06-08
  Type: Initial release
  
• Version 1.1: 2016-06-15
  Changes: Structure summary
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations, Structure summary