5CZD

The complex structure of VinK with VinL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-based analysis of the molecular interactions between acyltransferase and acyl carrier protein in vicenistatin biosynthesis.

Miyanaga, A.Iwasawa, S.Shinohara, Y.Kudo, F.Eguchi, T.

(2016) Proc.Natl.Acad.Sci.USA 113: 1802-1807

  • DOI: 10.1073/pnas.1520042113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Acyltransferases (ATs) are key determinants of building block specificity in polyketide biosynthesis. Despite the importance of protein-protein interactions between AT and acyl carrier protein (ACP) during the acyltransfer reaction, the mechanism of ...

    Acyltransferases (ATs) are key determinants of building block specificity in polyketide biosynthesis. Despite the importance of protein-protein interactions between AT and acyl carrier protein (ACP) during the acyltransfer reaction, the mechanism of ACP recognition by AT is not understood in detail. Herein, we report the crystal structure of AT VinK, which transfers a dipeptide group between two ACPs, VinL and VinP1LdACP, in vicenistatin biosynthesis. The isolated VinK structure showed a unique substrate-binding pocket for the dipeptide group linked to ACP. To gain greater insight into the mechanism of ACP recognition, we attempted to crystallize the VinK-ACP complexes. Because transient enzyme-ACP complexes are difficult to crystallize, we developed a covalent cross-linking strategy using a bifunctional maleimide reagent to trap the VinK-ACP complexes, allowing the determination of the crystal structure of the VinK-VinL complex. In the complex structure, Arg-153, Met-206, and Arg-299 of VinK interact with the negatively charged helix II region of VinL. The VinK-VinL complex structure allows, to our knowledge, the first visualization of the interaction between AT and ACP and provides detailed mechanistic insights into ACP recognition by AT.


    Organizational Affiliation

    Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan; eguchi@chem.titech.ac.jp miyanaga.a.aa@m.titech.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Malonyl-CoA-[acyl-carrier-protein] transacylase
A
343Streptomyces halstediiMutation(s): 1 
Gene Names: vinK
Find proteins for Q76KY5 (Streptomyces halstedii)
Go to UniProtKB:  Q76KY5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Acyl-carrier-protein
B
85Streptomyces halstediiMutation(s): 0 
Gene Names: vinL
Find proteins for Q76KY4 (Streptomyces halstedii)
Go to UniProtKB:  Q76KY4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1N2
Query on 1N2

Download SDF File 
Download CCD File 
B
1,1'-ethane-1,2-diyldipyrrolidine-2,5-dione
C10 H12 N2 O4
ZFMTZVFTWHQGNQ-UHFFFAOYSA-N
 Ligand Interaction
PNS
Query on PNS

Download SDF File 
Download CCD File 
B
4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.140α = 90.00
b = 68.230β = 90.00
c = 148.400γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
MOLREPphasing
SCALAdata scaling
Cootmodel building
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan15K18679

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-02-24
    Type: Database references
  • Version 1.2: 2016-03-30
    Type: Database references