5NNA

Isatin hydrolase A (IHA) from Labrenzia aggregata bound to benzyl benzoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
isatin hydrolase A
A, B, C, D
264Roseibium aggregatumMutation(s): 0 
Gene Names: SIAM614_30646
UniProt
Find proteins for A0P0F0 (Roseibium aggregatum (strain ATCC 25650 / DSM 13394 / JCM 20685 / NBRC 16684 / NCIMB 2208 / IAM 12614 / B1))
Explore A0P0F0 
Go to UniProtKB:  A0P0F0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0P0F0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
J [auth B]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
BZM
Query on BZM

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
L [auth C],
N [auth D]
BENZOIC ACID PHENYLMETHYLESTER
C14 H12 O2
SESFRYSPDFLNCH-UHFFFAOYSA-N
BTB
Query on BTB

Download Ideal Coordinates CCD File 
G [auth A]2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
K [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
M [auth C],
O [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.69α = 108.23
b = 70.67β = 95.94
c = 92.92γ = 101.48
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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