Isatin hydrolase A (IHA) from Ralstonia solanacearum

Experimental Data Snapshot

  • Resolution: 2.65 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


A fundamental catalytic difference between zinc and manganese dependent enzymes revealed in a bacterial isatin hydrolase.

Sommer, T.Bjerregaard-Andersen, K.Uribe, L.Etzerodt, M.Diezemann, G.Gauss, J.Cascella, M.Morth, J.P.

(2018) Sci Rep 8: 13104-13104

  • DOI: https://doi.org/10.1038/s41598-018-31259-y
  • Primary Citation of Related Structures:  
    5NMP, 5NNA, 5NNB

  • PubMed Abstract: 

    The catalytic mechanism of the cyclic amidohydrolase isatin hydrolase depends on a catalytically active manganese in the substrate-binding pocket. The Mn 2+ ion is bound by a motif also present in other metal dependent hydrolases like the bacterial kynurenine formamidase. The crystal structures of the isatin hydrolases from Labrenzia aggregata and Ralstonia solanacearum combined with activity assays allow for the identification of key determinants specific for the reaction mechanism. Active site residues central to the hydrolytic mechanism include a novel catalytic triad Asp-His-His supported by structural comparison and hybrid quantum mechanics/classical mechanics simulations. A hydrolytic mechanism for a Mn 2+ dependent amidohydrolases that disfavour Zn 2+ as the primary catalytically active site metal proposed here is supported by these likely cases of convergent evolution. The work illustrates a fundamental difference in the substrate-binding mode between Mn 2+ dependent isatin hydrolase like enzymes in comparison with the vast number of Zn 2+ dependent enzymes.

  • Organizational Affiliation

    Norwegian Center for Molecular Medicine, Nordic EMBL Partnership University of Oslo, Gaustadalléen 21, 0349, Oslo, Norway.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isatin hydrolase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
265Ralstonia pseudosolanacearum GMI1000Mutation(s): 0 
Gene Names: RSc1835
Find proteins for Q8XYC3 (Ralstonia nicotianae (strain GMI1000))
Explore Q8XYC3 
Go to UniProtKB:  Q8XYC3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8XYC3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SIN

Download Ideal Coordinates CCD File 
AA [auth I]
L [auth A]
N [auth B]
P [auth C]
R [auth D]
AA [auth I],
L [auth A],
N [auth B],
P [auth C],
R [auth D],
T [auth E],
V [auth F],
Y [auth H]
C4 H6 O4
Query on MN

Download Ideal Coordinates CCD File 
BA [auth J]
K [auth A]
M [auth B]
O [auth C]
Q [auth D]
BA [auth J],
K [auth A],
M [auth B],
O [auth C],
Q [auth D],
S [auth E],
U [auth F],
W [auth G],
X [auth H],
Z [auth I]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.65 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.84α = 90
b = 164.84β = 90
c = 275.89γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Research Council of NorwayNorwayES486454

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection
  • Version 1.2: 2018-09-12
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description