5YK9 | pdb_00005yk9

Crystal structure of selenomethionine-labelled indole prenyltransferase AmbP1

• PDB DOI: https://doi.org/10.2210/pdb5YK9/pdb

• Classification: TRANSFERASE
• Organism(s): Fischerella ambigua UTEX 1903
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-12 Released: 2018-06-06 
• Deposition Author(s): Awakawa, T., Nakashima, Y., Liu, X., Abe, I.
• Funding Organization(s): JSPS

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.265 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

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

• PubMed: 29677386 
• DOI: https://doi.org/10.1002/anie.201800855
• Primary Citation 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.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 70.68 kDa 
• Atom Count: 4,474 
• Modeled Residue Count: 584 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AmbP1	A, B	309	Fischerella ambigua UTEX 1903	Mutation(s): 0  Gene Names: ambP1, famD2
UniProt
Find proteins for V5TDZ4 (Fischerella ambigua (strain UTEX 1903)) Explore V5TDZ4  Go to UniProtKB:  V5TDZ4

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.265 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.259	α = 90
b = 142.35	β = 90
c = 157.147	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SHELXDE	phasing
Aimless	data scaling
XDS	data processing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-06-06 
Deposition Author(s): Awakawa, T., Nakashima, Y., Liu, X., Abe, I.

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Funding Organization	Location	Grant Number
JSPS	Japan	JP15H01836
JSPS	Japan	JP16H06443
JSPS	Japan	JP17H04763

Revision History  

• Version 1.0: 2018-06-06
  Type: Initial release
  
• Version 1.1: 2018-06-13
  Changes: Data collection, Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Structure summary