6LDL

Crystal structure of CYP116B46-N(20-445) from Tepidiphilus thermophilus in complex with HEME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structural insight into the electron transfer pathway of a self-sufficient P450 monooxygenase.

Zhang, L.Xie, Z.Liu, Z.Zhou, S.Ma, L.Liu, W.Huang, J.W.Ko, T.P.Li, X.Hu, Y.Min, J.Yu, X.Guo, R.T.Chen, C.C.

(2020) Nat Commun 11: 2676-2676

  • DOI: https://doi.org/10.1038/s41467-020-16500-5
  • Primary Citation of Related Structures:  
    6LAA, 6LDL

  • PubMed Abstract: 

    Cytochrome P450 monooxygenases are versatile heme-thiolate enzymes that catalyze a wide range of reactions. Self-sufficient cytochrome P450 enzymes contain the redox partners in a single polypeptide chain. Here, we present the crystal structure of full-length CYP116B46, a self-sufficient P450. The continuous polypeptide chain comprises three functional domains, which align well with the direction of electrons traveling from FMN to the heme through the [2Fe-2S] cluster. FMN and the [2Fe-2S] cluster are positioned closely, which facilitates efficient electron shuttling. The edge-to-edge straight-line distance between the [2Fe-2S] cluster and heme is approx. 25.3 Å. The role of several residues located between the [2Fe-2S] cluster and heme in the catalytic reaction is probed in mutagenesis experiments. These findings not only provide insights into the intramolecular electron transfer of self-sufficient P450s, but are also of interest for biotechnological applications of self-sufficient P450s.


  • Organizational Affiliation

    State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, P. R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450426Tepidiphilus thermophilusMutation(s): 0 
Gene Names: Ga0061068_103196
UniProt
Find proteins for A0A0K6ITW2 (Tepidiphilus thermophilus)
Explore A0A0K6ITW2 
Go to UniProtKB:  A0A0K6ITW2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K6ITW2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.471α = 90
b = 75.511β = 90
c = 105.148γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description