5Z46

Crystal structure of prenyltransferase AmbP1 pH8 complexed with GSPP and cis-indolyl vinyl isonitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.235 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

Molecular Insight into the Mg2+-Dependent Allosteric Control of Indole Prenylation by Aromatic Prenyltransferase AmbP1

Awakawa, T.Mori, T.Nakashima, Y.Zhai, R.Wong, C.P.Hillwig, M.L.Liu, X.Abe, I.

(2018) Angew Chem Int Ed Engl 57: 6810-6813

  • DOI: https://doi.org/10.1002/anie.201800855
  • Primary Citation of Related Structures:  
    5YK9, 5Z43, 5Z44, 5Z45, 5Z46

  • PubMed Abstract: 

    AmbP1 is a cyanobacterial aromatic prenyltransferase and a dedicated synthase for (R)-3-geranyl-3-isocyanovinyl indolenine (2), the biogenetic precursor for hapalindole-type alkaloids. The regioselective geranylation of cis-indolyl vinyl isonitrile (1) by the standalone AmbP1 to give 2 has been shown to require a magnesium ion (Mg 2+ ) to suppress the formation of cis-2-geranylindolyl vinyl isonitrile (3). Here, we report high-resolution crystal structures of AmbP1 in complex with 1 and geranyl S-thiodiphosphate (GSPP) in the presence and absence of a Mg 2+ effector. The comparative study of these structures revealed a unique allosteric binding site for Mg 2+ that modulates the conformation of 1 in the active site of AmbP1 for its selective geranylation. This work defines the structural basis for AmbP1 catalysis in the biogenesis of hapalindole-type alkaloids and provides the first atomic-level insight to the allosteric regulation of prenyltransferases.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AmbP1
A, B
309Fischerella ambigua UTEX 1903Mutation(s): 0 
Gene Names: ambP1famD2
UniProt
Find proteins for V5TDZ4 (Fischerella ambigua (strain UTEX 1903))
Explore V5TDZ4 
Go to UniProtKB:  V5TDZ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupV5TDZ4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.267α = 90
b = 117.267β = 90
c = 49.324γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted GSTClick on this verticalbar to view detailsBest fitted 8XLClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-06-13
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description