4UB9

Structural and catalytic characterization of molinate hydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-guided engineering of molinate hydrolase for the degradation of thiocarbamate pesticides.

Leite, J.P.Duarte, M.Paiva, A.M.Ferreira-da-Silva, F.Matias, P.M.Nunes, O.C.Gales, L.

(2015) Plos One 10: e0123430-e0123430

  • DOI: 10.1371/journal.pone.0123430

  • PubMed Abstract: 
  • Molinate is a recalcitrant thiocarbamate used to control grass weeds in rice fields. The recently described molinate hydrolase, from Gulosibacter molinativorax ON4T, plays a key role in the only known molinate degradation pathway ending in the format ...

    Molinate is a recalcitrant thiocarbamate used to control grass weeds in rice fields. The recently described molinate hydrolase, from Gulosibacter molinativorax ON4T, plays a key role in the only known molinate degradation pathway ending in the formation of innocuous compounds. Here we report the crystal structure of recombinant molinate hydrolase at 2.27 Å. The structure reveals a homotetramer with a single mononuclear metal-dependent active site per monomer. The active site architecture shows similarities with other amidohydrolases and enables us to propose a general acid-base catalysis mechanism for molinate hydrolysis. Molinate hydrolase is unable to degrade bulkier thiocarbamate pesticides such as thiobencarb which is used mostly in rice crops. Using a structural-based approach, we were able to generate a mutant (Arg187Ala) that efficiently degrades thiobencarb. The engineered enzyme is suitable for the development of a broader thiocarbamate bioremediation system.


    Organizational Affiliation

    Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Molinate hydrolase
A, B, C, D, E, F, G, H
496Gulosibacter molinativoraxMutation(s): 0 
Gene Names: molA
Find proteins for G2XLB0 (Gulosibacter molinativorax)
Go to UniProtKB:  G2XLB0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 367.696α = 90.00
b = 99.079β = 109.61
c = 131.337γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
SHARPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
FCTPortugalFCOMP-01-0124-FEDER-027883 (PTDC/AAGTEC/3909/2012FCOMP)

Revision History 

  • Version 1.0: 2015-06-24
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Advisory, Data collection, Derived calculations