5Z9I

Identification of the functions of unusual cytochrome p450-like monooxygenases involved in microbial secondary metablism


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.188 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Riboflavin Is Directly Involved in the N-Dealkylation Catalyzed by Bacterial Cytochrome P450 Monooxygenases.

Zhang, C.Lu, M.Lin, L.Huang, Z.Zhang, R.Wu, X.Chen, Y.

(2020) Chembiochem 

  • DOI: 10.1002/cbic.202000071
  • Primary Citation of Related Structures:  
    5Z9I, 5Z9J

  • PubMed Abstract: 
  • Like a vast number of enzymes in nature, bacterial cytochrome P450 monooxygenases require an activated form of flavin as a cofactor for catalytic activity. Riboflavin is the precursor of FAD and FMN that serves as indispensable cofactor for flavoenzymes. In contrast to previous notions, herein we describe the identification of an electron-transfer process that is directly mediated by riboflavin for N-dealkylation by bacterial P450 monooxygenases ...

    Like a vast number of enzymes in nature, bacterial cytochrome P450 monooxygenases require an activated form of flavin as a cofactor for catalytic activity. Riboflavin is the precursor of FAD and FMN that serves as indispensable cofactor for flavoenzymes. In contrast to previous notions, herein we describe the identification of an electron-transfer process that is directly mediated by riboflavin for N-dealkylation by bacterial P450 monooxygenases. The electron relay from NADPH to riboflavin and then via activated oxygen to heme was proposed based on a combination of X-ray crystallography, molecular modeling and molecular dynamics simulation, site-directed mutagenesis and biochemical analysis of representative bacterial P450 monooxygenases. This study provides new insights into the electron transfer mechanism in bacterial P450 enzyme catalysis and likely in yeasts, fungi, plants and mammals.


    Organizational Affiliation

    Laboratory of Chemical Biology and State Key Laboratory of Natural Medicines, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu Province, 211198, P. R. China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative P450-like enzymeA398Streptomyces himastatinicus ATCC 53653Mutation(s): 1 
Gene Names: hmtS
UniProt
Find proteins for G0LWB2 (Streptomyces himastatinicus ATCC 53653)
Explore G0LWB2 
Go to UniProtKB:  G0LWB2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.987α = 90
b = 72.492β = 90
c = 98.829γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
DENZOdata 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: 2019-02-06
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references