5CZC | pdb_00005czc

The structure of VinK

• PDB DOI: https://doi.org/10.2210/pdb5CZC/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces halstedii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-31 Released: 2016-02-03 
• Deposition Author(s): Miyanaga, A., Iwasawa, S., Shinohara, Y., Kudo, F., Eguchi, T.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.216 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

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

• PubMed: 26831085 
• DOI: https://doi.org/10.1073/pnas.1520042113
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan; [e-mail] [e-mail].
Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan;
Department of Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan.
Department of Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan [e-mail] [e-mail].

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: 72.78 kDa 
• Atom Count: 5,101 
• Modeled Residue Count: 601 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malonyl-CoA-[acyl-carrier-protein] transacylase	A, B	328	Streptomyces halstedii	Mutation(s): 0  Gene Names: vinK EC: 2.3.1.39
UniProt
Find proteins for Q76KY5 (Streptomyces halstedii) Explore Q76KY5  Go to UniProtKB:  Q76KY5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	D [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.216 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.52	α = 90
b = 74.81	β = 91.24
c = 84.81	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Miyanaga, A., Iwasawa, S., Shinohara, Y., Kudo, F., Eguchi, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	15K18679

Revision History  

• 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: 2024-03-20
  Changes: Data collection, Database references, Derived calculations