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 
  • R-Value Observed: 0.202 

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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
  • Primary Citation of Related Structures:  
    4UB9

  • 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; ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Molinate hydrolaseABCDEFGH496Gulosibacter molinativoraxMutation(s): 0 
Gene Names: molA
Find proteins for G2XLB0 (Gulosibacter molinativorax)
Explore G2XLB0 
Go to UniProtKB:  G2XLB0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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 
  • R-Value Observed: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 367.696α = 90
b = 99.079β = 109.61
c = 131.337γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SHARPphasing
XSCALEdata scaling

Structure Validation

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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
    Changes: Advisory, Data collection, Derived calculations