Cytochrome P450 monooxygenase StvP2 substrate-free structure

Experimental Data Snapshot

  • Resolution: 1.35 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.139 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Uncovering the cytochrome P450-catalyzed methylenedioxy bridge formation in streptovaricins biosynthesis.

Sun, G.Hu, C.Mei, Q.Luo, M.Chen, X.Li, Z.Liu, Y.Deng, Z.Zhang, Z.Sun, Y.

(2020) Nat Commun 11: 4501-4501

  • DOI: https://doi.org/10.1038/s41467-020-18336-5
  • Primary Citation of Related Structures:  
    6M4P, 6M4Q

  • PubMed Abstract: 

    Streptovaricin C is a naphthalenic ansamycin antibiotic structurally similar to rifamycins with potential anti-MRSA bioactivities. However, the formation mechanism of the most fascinating and bioactivity-related methylenedioxy bridge (MDB) moiety in streptovaricins is unclear. Based on genetic and biochemical evidences, we herein clarify that the P450 enzyme StvP2 catalyzes the MDB formation in streptovaricins, with an atypical substrate inhibition kinetics. Furthermore, X-ray crystal structures in complex with substrate and structure-based mutagenesis reveal the intrinsic details of the enzymatic reaction. The mechanism of MDB formation is proposed to be an intramolecular nucleophilic substitution resulting from the hydroxylation by the heme core and the keto-enol tautomerization via a crucial catalytic triad (Asp89-His92-Arg72) in StvP2. In addition, in vitro reconstitution uncovers that C6-O-methylation and C4-O-acetylation of streptovaricins are necessary prerequisites for the MDB formation. This work provides insight for the MDB formation and adds evidence in support of the functional versatility of P450 enzymes.

  • Organizational Affiliation

    Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 430071, Wuhan, P. R. China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450401Streptomyces spectabilisMutation(s): 0 
Gene Names: stvP2
Find proteins for A0A286SBY7 (Streptomyces spectabilis)
Explore A0A286SBY7 
Go to UniProtKB:  A0A286SBY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A286SBY7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
C34 H32 Fe N4 O4
Experimental Data & Validation

Experimental Data

  • Resolution: 1.35 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.139 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.073α = 90
b = 145.716β = 90
c = 90.447γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2018YFA0903200
National Natural Science Foundation of China (NSFC)China31800052

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description