4UB9 | pdb_00004ub9

Structural and catalytic characterization of molinate hydrolase

PDB DOI: https://doi.org/10.2210/pdb4UB9/pdb

Classification: HYDROLASE
Organism(s): Gulosibacter molinativorax
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-08-12 Released: 2015-06-24
Deposition Author(s): Leite, J.P., Duarte, M., Paiva, A., Ferreira-da-Silva, F., Matias, P.M., Nunes, O., Gales, L.
Funding Organization(s): FCT

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.229 (Depositor), 0.233 (DCC)
R-Value Work:
0.201 (Depositor), 0.207 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 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

PubMed: 25905461 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0123430
Primary Citation 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 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.

Macromolecule Content

Total Structure Weight: 437.96 kDa
Atom Count: 29,391
Modeled Residue Count: 3,736
Deposited Residue Count: 3,968
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Molinate hydrolase	A, B, C, D, E A, B, C, D, E, F, G, H	496	Gulosibacter molinativorax	Mutation(s): 0 Gene Names: molA
UniProt
Find proteins for G2XLB0 (Gulosibacter molinativorax) Explore G2XLB0 Go to UniProtKB: G2XLB0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G2XLB0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain N [auth F] SDF format, chain O [auth G] SDF format, chain P [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F] MOL2 format, chain O [auth G] MOL2 format, chain P [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth E] mmCIF format, chain N [auth F] mmCIF format, chain O [auth G] mmCIF format, chain P [auth H]	I [auth A] J [auth B] K [auth C] L [auth D] M [auth E] I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.229 (Depositor), 0.233 (DCC)
R-Value Work: 0.201 (Depositor), 0.207 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 367.696	α = 90
b = 99.079	β = 109.61
c = 131.337	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SHARP	phasing
XSCALE	data scaling

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-06-24

Deposition Author(s):

Leite, J.P.

Duarte, M.

Paiva, A.

Ferreira-da-Silva, F.

Matias, P.M.

Nunes, O.

Gales, L.

Funding Organization	Location	Grant Number
FCT	Portugal	FCOMP-01-0124-FEDER-027883 (PTDC/AAGTEC/3909/2012FCOMP)

Revision History (Full details and data files)

Version 1.0: 2015-06-24
Type: Initial release
Version 1.1: 2019-02-20
Changes: Advisory, Data collection, Derived calculations
Version 1.2: 2024-05-01
Changes: Data collection, Database references, Derived calculations, Refinement description