4J0N

Crystal structure of a manganese dependent isatin hydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A proton wire and water channel revealed in the crystal structure of isatin hydrolase.

Bjerregaard-Andersen, K.Sommer, T.Jensen, J.K.Jochimsen, B.Etzerodt, M.Morth, J.P.

(2014) J.Biol.Chem. 289: 21351-21359

  • DOI: 10.1074/jbc.M114.568824
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The high resolution crystal structures of isatin hydrolase from Labrenzia aggregata in the apo and the product state are described. These are the first structures of a functionally characterized metal-dependent hydrolase of this fold. Isatin hydrolas ...

    The high resolution crystal structures of isatin hydrolase from Labrenzia aggregata in the apo and the product state are described. These are the first structures of a functionally characterized metal-dependent hydrolase of this fold. Isatin hydrolase converts isatin to isatinate and belongs to a novel family of metalloenzymes that include the bacterial kynurenine formamidase. The product state, mimicked by bound thioisatinate, reveals a water molecule that bridges the thioisatinate to a proton wire in an adjacent water channel and thus allows the proton released by the reaction to escape only when the product is formed. The functional proton wire present in isatin hydrolase isoform b represents a unique catalytic feature common to all hydrolases is here trapped and visualized for the first time. The local molecular environment required to coordinate thioisatinate allows stronger and more confident identification of orthologous genes encoding isatin hydrolases within the prokaryotic kingdom. The isatin hydrolase orthologues found in human gut bacteria raise the question as to whether the indole-3-acetic acid degradation pathway is present in human gut flora.


    Organizational Affiliation

    From the Norwegian Center of Molecular Medicine, Nordic EMBL Partnership University of Oslo, Gaustadalléen 21, 0349 Oslo, Norway, the Department for Molecular Biology and Genetics, Aarhus University, Gustav Wieds vej 10C, DK-8000 Aarhus, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Isatin hydrolase B
A, B
263Labrenzia aggregata (strain ATCC 25650 / DSM 13394 / JCM 20685 / NBRC 16684 / NCIMB 2208 / IAM 12614)Mutation(s): 0 
EC: 3.5.2.20
Find proteins for A0NLY7 (Labrenzia aggregata (strain ATCC 25650 / DSM 13394 / JCM 20685 / NBRC 16684 / NCIMB 2208 / IAM 12614))
Go to UniProtKB:  A0NLY7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.171 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 51.940α = 90.00
b = 51.940β = 90.00
c = 176.690γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXmodel building
PHENIXrefinement
xia2data scaling
MxCuBEdata collection
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2014-07-16
    Type: Database references
  • Version 1.2: 2014-08-20
    Type: Database references
  • Version 1.3: 2018-03-07
    Type: Data collection