3WMR

Crystal structure of VinJ


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1016/j.febslet.2014.01.060

  • 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. V ...

    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.


    Organizational Affiliation

    Department of Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan.,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. Electronic address: eguchi@cms.titech.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proline iminopeptidase
A, B, C
315Streptomyces halstediiMutation(s): 0 
Gene Names: vinJ
Find proteins for Q76KY6 (Streptomyces halstedii)
Go to UniProtKB:  Q76KY6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
P4G
Query on P4G

Download SDF File 
Download CCD File 
A, B
1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
C8 H18 O3
RRQYJINTUHWNHW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.165 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 52.870α = 114.02
b = 72.620β = 98.39
c = 75.450γ = 98.50
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
ADSCdata collection
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2014-03-19
    Type: Database references