6U9I

Crystal structure of BvnE pinacolase from Penicillium brevicompactum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

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This is version 1.2 of the entry. See complete history


Literature

Fungal-derived brevianamide assembly by a stereoselective semipinacolase.

Ye, Y.Du, L.Zhang, X.Newmister, S.A.McCauley, M.Alegre-Requena, J.V.Zhang, W.Mu, S.Minami, A.Fraley, A.E.Adrover-Castellano, M.L.Carney, N.A.Shende, V.V.Qi, F.Oikawa, H.Kato, H.Tsukamoto, S.Paton, R.S.Williams, R.M.Sherman, D.H.Li, S.

(2020) Nat Catal 3: 497-506

  • DOI: https://doi.org/10.1038/s41929-020-0454-9
  • Primary Citation of Related Structures:  
    6U9I

  • PubMed Abstract: 

    Fungal bicyclo[2.2.2]diazaoctane indole alkaloids represent an important family of natural products with a wide-spectrum of biological activities. Although biomimetic total syntheses of representative compounds have been reported, the details of their biogenesis, especially the mechanisms for assembly of diastereomerically distinct and enantiomerically antipodal metabolites, have remained largely uncharacterized. Brevianamide A represents a basic form of the sub-family bearing a dioxopiperazine core and a rare 3- spiro -ψ-indoxyl skeleton. Here, we identified the Brevianamide A biosynthetic gene cluster from Penicillium brevicompactum NRRL 864 and elucidated the metabolic pathway. BvnE was revealed to be an essential isomerase/semi-pinacolase that specifies selective production of the natural product. Structural elucidation, molecular modeling, and mutational analysis of BvnE, and quantum chemical calculations provided mechanistic insights into the diastereoselective formation of the 3- spiro -ψ-indoxyl moiety in Brevianamide A. This occurs through a BvnE-controlled semi-pinacol rearrangement and a subsequent spontaneous intramolecular [4+2] hetero -Diels-Alder cycloaddition.


  • Organizational Affiliation

    Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BvnE
A, B
157Penicillium brevicompactumMutation(s): 0 
UniProt
Find proteins for A0A5Q0MV05 (Penicillium brevicompactum)
Explore A0A5Q0MV05 
Go to UniProtKB:  A0A5Q0MV05
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5Q0MV05
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.58α = 90
b = 105.58β = 90
c = 61.648γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA070375
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118101
National Natural Science Foundation of China (NSFC)China21472204
National Natural Science Foundation of China (NSFC)China31800041

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-09
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description