9LN5 | pdb_00009ln5

Crystal structure of P450revI A241L mutant in complex with reveromycin T


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 
    0.274 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

Starting Model: experimental
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Literature

Biosynthesis of reveromycin derivatives by altering the regioselectivity of cytochrome P450revI.

Yong, Y.F.Liu, S.Sakai, K.Fujiyama, K.Takagi, H.Futamura, Y.Shimizu, T.Osada, H.Ong, E.B.B.Takahashi, S.

(2025) Chem Sci 16: 13106-13114

  • DOI: https://doi.org/10.1039/d5sc01355k
  • Primary Citation of Related Structures:  
    9LN5

  • PubMed Abstract: 

    Reveromycin A (RM-A) (1) has a 6,6-spiroacetal core structure that is important for its biological activity. However, 1 undergoes a spiroacetal rearrangement to form RM-B (2) with a 5,6-spiroacetal core, which exhibits reduced bioactivity. This undesired rearrangement is partly due to the hemisuccinate moiety at the C18 position of 1. In 1 biosynthesis, P450revI catalyses the C18-hydroxylation of RM-T (3), which is essential for its subsequent hemisuccinylation to generate 1. In this study, we aimed to alter the P450revI regioselectivity to improve the stability of the 6,6-spiroacetal core and expand the structural diversity of RMs. Candidate amino acid residues for mutagenesis studies were selected by comparing the co-crystal structure of P450revI with the docking models of the P450revI mutant-3 complexes. Notably, the P450revI-A241L mutant selectively produced novel RM derivatives. Nuclear magnetic resonance analysis revealed that P450revI-A241L catalysed the C17-hydroxylation of 3 to produce 17-hydroxy-RM-T (6). Co-crystal structure analysis of the P450revI-A241L-3 complex revealed that the pro- R hydrogen at the C17 position faces toward the haem iron. Introduction of the P450revI-A241L mutant gene into the Actinacidiphila reveromycinica SN-593-Δ revI strain led to the production of 17-hemisuccinyloxy-RM-T (7). After the successful bioproduction of RM derivatives, we evaluated their structural stabilities and biological activities. Compounds 6 and 7 exhibited better stabilities than 18-hydroxylated-3 (RM-T1; 4) and 1, respectively. Biological activity analysis revealed that 6 and 7 exhibited anti-malarial and anti-multiple myeloma activities, respectively, comparable to those of 1 and 3, while showing low cytotoxicity against human cell lines. Overall, this study highlights the potential of RM derivatives as pharmaceuticals.


  • Organizational Affiliation
    • Natural Product Biosynthesis Research Unit, RIKEN Center for Sustainable Resource Science Wako Saitama 351-0198 Japan shunjitaka@riken.jp.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative monooxygenase401Actinacidiphila reveromycinicaMutation(s): 1 
Gene Names: revIRVR_8636
UniProt
Find proteins for G1UDU7 (Actinacidiphila reveromycinica)
Explore G1UDU7 
Go to UniProtKB:  G1UDU7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1UDU7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free:  0.274 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.791α = 90
b = 72.791β = 90
c = 348.37γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
pointlessdata scaling
Aimlessdata scaling
PHASERphasing
Cootmodel building
REFMACrefinement
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan20H00416

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2025-07-30
    Changes: Database references