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 
  • R-Value Observed: 0.205 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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 U S A 113: 1802-1807

  • DOI: https://doi.org/10.1073/pnas.1520042113
  • Primary Citation of Related Structures:  
    5CZC, 5CZD

  • 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 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; [email protected] [email protected].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Malonyl-CoA-[acyl-carrier-protein] transacylase343Streptomyces halstediiMutation(s): 1 
Gene Names: vinK
EC: 2.3.1.39
UniProt
Find proteins for Q76KY5 (Streptomyces halstedii)
Explore Q76KY5 
Go to UniProtKB:  Q76KY5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ76KY5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl-carrier-protein85Streptomyces halstediiMutation(s): 0 
Gene Names: vinL
UniProt
Find proteins for Q76KY4 (Streptomyces halstedii)
Explore Q76KY4 
Go to UniProtKB:  Q76KY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ76KY4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PNS
Query on PNS

Download Ideal Coordinates CCD File 
C [auth B]4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
1N2
Query on 1N2

Download Ideal Coordinates CCD File 
D [auth B]1,1'-ethane-1,2-diyldipyrrolidine-2,5-dione
C10 H12 N2 O4
ZFMTZVFTWHQGNQ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.14α = 90
b = 68.23β = 90
c = 148.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan15K18679

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-02-24
    Changes: Database references
  • Version 1.2: 2016-03-30
    Changes: Database references
  • Version 1.3: 2020-02-19
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description