5YM3

CYP76AH1-4pi from salvia miltiorrhiza


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

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Literature

Crystal structure of CYP76AH1 in 4-PI-bound state from Salvia miltiorrhiza.

Gu, M.Wang, M.Guo, J.Shi, C.Deng, J.Huang, L.Huang, L.Chang, Z.

(2019) Biochem Biophys Res Commun 511: 813-819

  • DOI: 10.1016/j.bbrc.2019.02.103
  • Primary Citation of Related Structures:  
    5YM3

  • PubMed Abstract: 
  • Tanshinones are important diterpenoid secondary metabolites from Salvia miltiorrhiza, widely used as cardiovascular and cerebrovascular medicines. CYP76AH1 is a membrane-associated cytochrome P450 enzyme and plays a critical role in the biosynthetic pathway of tanshinones ...

    Tanshinones are important diterpenoid secondary metabolites from Salvia miltiorrhiza, widely used as cardiovascular and cerebrovascular medicines. CYP76AH1 is a membrane-associated cytochrome P450 enzyme and plays a critical role in the biosynthetic pathway of tanshinones. To clarify the relationship between structure and function of CYP76AH1, we recently constructed the expression vector of CYP76AH1 and purified the enzyme. The engineered CYP76AH1 was expressed in E. coli Trans-blue cells and exhibited enhanced expression and solubility. The proper folding of the engineered CYP76AH1 was assessed by CO difference spectrum assay. Functional identification of the recombinant enzyme was performed by conducting enzymatic reaction with the purified CYP76AH1 in presence of substrate, the co-factor NADPH and the purified SmCPR1 (cytochrome P450 reductase from Salvia miltiorrhiza), and by subsequently analyzing the reaction extract through GC-MS. X-ray crystal complex structure of CYP76AH1 with inhibitor 4-phenylimmidazole (4-PI) was determined at the resolution of 2.6 Å. In the ligand-binding cavity of 4-PI bound CYP76AH1, the inhibitor 4-PI forms a hydrogen bound with a water molecule which coordinates with heme at the sixth coordination position. There are two open channels which substrate and product site may access and leave the active site. In the CYP76AH1/4-PI complex structure, the imidazole ring of 4-PI is parallel to helix I instead of perpendicular to helies I in most P450s bound imidazole. 4-PI may be work in the stability of CYP76AH1 crystal structure. These studies provide information on functional expression and purification of CYP76AH1, and overall structure of CYP76AH1 complexed with 4-PI.


    Organizational Affiliation

    Department of Biophysics, School of Basic Medical Sciences, Peking University, Beijing, 100191, China. Electronic address: changz@bjmu.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ferruginol synthaseA495Salvia miltiorrhizaMutation(s): 0 
Gene Names: CYP76AH1
EC: 1.14.13.190
UniProt
Find proteins for S4UX02 (Salvia miltiorrhiza)
Explore S4UX02 
Go to UniProtKB:  S4UX02
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / 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
 Ligand Interaction
PIM
Query on PIM

Download Ideal Coordinates CCD File 
C [auth A]4-PHENYL-1H-IMIDAZOLE
C9 H8 N2
XHLKOHSAWQPOFO-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
D [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.103α = 90
b = 109.103β = 90
c = 105.709γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-10-20 
  • Released Date: 2018-10-24 
  • Deposition Author(s): Chang, Z.

Funding OrganizationLocationGrant Number
The National Natural Science Foundation of ChinaChina81773833

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references