3X27

Structure of McbB in complex with tryptophan


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

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This is version 1.1 of the entry. See complete history


Literature

Structural Basis for beta-Carboline Alkaloid Production by the Microbial Homodimeric Enzyme McbB

Mori, T.Hoshino, S.Sahashi, S.Wakimoto, T.Matsui, T.Morita, H.Abe, I.

(2015) Chem Biol 22: 898-906

  • DOI: https://doi.org/10.1016/j.chembiol.2015.06.006
  • Primary Citation of Related Structures:  
    3X27

  • PubMed Abstract: 

    The β-carboline (βC) alkaloids occur throughout nature and exhibit diverse biological activities. In contrast to βC alkaloid synthesis in plants, the biosynthesis in microorganisms remains poorly understood. The recently reported McbB from Marinactinospora thermotolerans is a novel enzyme proposed to catalyze the Pictet-Spengler (PS) reaction of L-tryptophan and oxaloacetaldehyde to produce the βC scaffold of marinacarbolines. In this study, we solved the crystal structure of McbB complexed with L-tryptophan at 2.48 Å resolution, which revealed the novel protein folding of McbB and the totally different structure from those of other PS condensation catalyzing enzymes, such as strictosidine synthase and norcoclaurine synthase from plants. Structural analysis and site-directed mutagenesis confirmed that the previously proposed catalytic Glu97 at the active-site center functions as an acid and base catalyst. Remarkably, the structure-based mutants R72A and H87A, with expanded active-site cavities, newly accepted bulky phenylglyoxal as the aldehyde substrate, to produce 1-benzoyl-3-carboxy-β-carboline.


  • Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cucumopine synthase
A, B, C, D
335Marinactinospora thermotoleransMutation(s): 0 
UniProt
Find proteins for R4QPW9 (Marinactinospora thermotolerans)
Explore R4QPW9 
Go to UniProtKB:  R4QPW9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4QPW9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.76α = 90
b = 108.81β = 90
c = 146.36γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
AutoSolphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2015-11-04
    Changes: Other