3WMR

Crystal structure of VinJ

• PDB DOI: https://doi.org/10.2210/pdb3WMR/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces halstedii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-11-22 Released: 2014-02-05 
• Deposition Author(s): Shinohara, Y., Miyanaga, A., Kudo, F., Eguchi, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.206 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Literature

The crystal structure of the amidohydrolase VinJ shows a unique hydrophobic tunnel for its interaction with polyketide substrates

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

(2014) FEBS Lett 588: 995-1000

• PubMed: 24530530 
• DOI: https://doi.org/10.1016/j.febslet.2014.01.060
• Primary Citation of Related Structures:  
  3WMR


• PubMed Abstract: 
  

  VinJ is an amidohydrolase belonging to the serine peptidase family that catalyzes the hydrolysis of the terminal aminoacyl moiety of a polyketide intermediate during the biosynthesis of vicenistatin. Herein, we report the crystal structure of VinJ. VinJ possesses a unique hydrophobic tunnel for the recognition of the polyketide chain moiety of its substrate in the cap domain. Taken together with the results of phylogenetic analysis, our results suggest that VinJ represents a new amidohydrolase family that is different from the known α/β hydrolase type serine peptidases.

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Organizational Affiliation: 

Department of Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 107.71 kDa 
• Atom Count: 7,591 
• Modelled Residue Count: 888 
• Deposited Residue Count: 945 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline iminopeptidase	A, B, C	315	Streptomyces halstedii	Mutation(s): 0  Gene Names: vinJ
UniProt
Find proteins for Q76KY6 (Streptomyces halstedii) Explore Q76KY6  Go to UniProtKB:  Q76KY6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P4G	E [auth A], H [auth B]	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE C8 H18 O3 RRQYJINTUHWNHW-UHFFFAOYSA-N
GOL	D [auth A], F [auth B], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.206 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.87	α = 114.02
b = 72.62	β = 98.39
c = 75.45	γ = 98.5

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-05 
Deposition Author(s): Shinohara, Y., Miyanaga, A., Kudo, F., Eguchi, T.

Revision History  

• Version 1.0: 2014-02-05
  Type: Initial release
  
• Version 1.1: 2014-03-19
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description