6VXV

Crystal structure of cyclo-L-Trp-L-Pro-bound cytochrome P450 NasF5053 from Streptomyces sp. NRRL F-5053


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


Literature

Molecular basis of regio- and stereo-specificity in biosynthesis of bacterial heterodimeric diketopiperazines.

Sun, C.Luo, Z.Zhang, W.Tian, W.Peng, H.Lin, Z.Deng, Z.Kobe, B.Jia, X.Qu, X.

(2020) Nat Commun 11: 6251-6251

  • DOI: https://doi.org/10.1038/s41467-020-20022-5
  • Primary Citation of Related Structures:  
    6VXV, 6VZA, 6VZB, 6W0S

  • PubMed Abstract: 

    Bacterial heterodimeric tryptophan-containing diketopiperazines (HTDKPs) are a growing family of bioactive natural products. They are challenging to prepare by chemical routes due to the polycyclic and densely functionalized backbone. Through functional characterization and investigation, we herein identify a family of three related HTDKP-forming cytochrome P450s (NasbB, Nas S1868 and Nas F5053 ) and reveal four critical residues (Qln65, Ala86, Ser284 and Val288) that control their regio- and stereo-selectivity to generate diverse dimeric DKP frameworks. Engineering these residues can alter the specificities of the enzymes to produce diverse frameworks. Determining the crystal structures (1.70-1.47 Å) of Nas F5053 (ligand-free and substrate-bound Nas F5053 and its Q65I-A86G and S284A-V288A mutants) and molecular dynamics simulation finally elucidate the specificity-conferring mechanism of these residues. Our results provide a clear molecular and mechanistic basis into this family of HTDKP-forming P450s, laying a solid foundation for rapid access to the molecular diversity of HTDKP frameworks through rational engineering of the P450s.


  • Organizational Affiliation

    State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cytochrome P450 NasF5053398Streptomyces sp. NRRL F-5053Mutation(s): 0 
EC: 1.14
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.314α = 90
b = 91.836β = 90
c = 93.604γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1071659
National Natural Science Foundation of China (NSFC)China31770063

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description