8TWU

Crystal structure of Cytochrome P450 AspB bound to N1-methylated cyclo-L-Trp-L-Pro


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

Starting Model: experimental
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Literature

A Ferric-Superoxide Intermediate Initiates P450-Catalyzed Cyclic Dipeptide Dimerization.

Gering, H.E.Li, X.Tang, H.Swartz, P.D.Chang, W.C.Makris, T.M.

(2023) J Am Chem Soc 145: 19256-19264

  • DOI: https://doi.org/10.1021/jacs.3c04542
  • Primary Citation of Related Structures:  
    8TWU

  • PubMed Abstract: 

    The cytochrome P450 (CYP) AspB is involved in the biosynthesis of the diketopiperazine (DKP) aspergilazine A. Tryptophan-linked dimeric DKP alkaloids are a large family of natural products that are found in numerous species and exhibit broad and often potent bioactivity. The proposed mechanisms for C-N bond formation by AspB, and similar C-C bond formations by related CYPs, have invoked the use of a ferryl-intermediate as an oxidant to promote substrate dimerization. Here, the parallel application of steady-state and transient kinetic approaches reveals a very different mechanism that involves a ferric-superoxide species as a primary oxidant to initiate DKP-assembly. Single turnover kinetic isotope effects and a substrate analog suggest the probable nature and site for abstraction. The direct observation of CYP-superoxide reactivity rationalizes the atypical outcome of AspB and reveals a new reaction manifold in heme enzymes.


  • Organizational Affiliation

    Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450 AspB407StreptomycesMutation(s): 0 
UniProt
Find proteins for A0A9X9ZA09 (Streptomyces sp. NRRL S-1868)
Explore A0A9X9ZA09 
Go to UniProtKB:  A0A9X9ZA09
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A9X9ZA09
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.71α = 90
b = 120.999β = 90
c = 46.223γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM135315
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM127588

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-20
    Type: Initial release