6CGY | pdb_00006cgy

Structure of the Quorum Quenching lactonase from Alicyclobacillus acidoterrestris bound to a phosphate anion

PDB DOI: https://doi.org/10.2210/pdb6CGY/pdb

Classification: HYDROLASE
Organism(s): Alicyclobacillus acidoterrestris ATCC 49025
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-02-21 Released: 2018-08-15
Deposition Author(s): Bergonzi, C., Schwab, M., Naik, T., Daude, D., Chabriere, E., Elias, M.
Funding Organization(s): MnDrive

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.197 (Depositor), 0.205 (DCC)
R-Value Work:
0.170 (Depositor), 0.181 (DCC)
R-Value Observed:
0.172 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural and Biochemical Characterization of AaL, a Quorum Quenching Lactonase with Unusual Kinetic Properties.

Bergonzi, C., Schwab, M., Naik, T., Daude, D., Chabriere, E., Elias, M.

(2018) Sci Rep 8: 11262-11262

PubMed: 30050039 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41598-018-28988-5
Primary Citation Related Structures:
6CGY, 6CGZ, 6CH0

PubMed Abstract:
Quorum quenching lactonases are enzymes that are capable of disrupting bacterial signaling based on acyl homoserine lactones (AHL) via their enzymatic degradation. In particular, lactonases have therefore been demonstrated to inhibit bacterial behaviors that depend on these chemicals, such as the formation of biofilms or the expression of virulence factors. Here we characterized biochemically and structurally a novel representative from the metallo-β-lactamase superfamily, named AaL that was isolated from the thermoacidophilic bacterium Alicyclobacillus acidoterrestris. AaL is a potent quorum quenching enzyme as demonstrated by its ability to inhibit the biofilm formation of Acinetobacter baumannii. Kinetic studies demonstrate that AaL is both a proficient and a broad spectrum enzyme, being capable of hydrolyzing a wide range of lactones with high rates (k _cat/K _M > 10 ⁵ M ^-1.s ^-1). Additionally, AaL exhibits unusually low K _M values, ranging from 10 to 80 µM. Analysis of AaL structures bound to phosphate, glycerol, and C6-AHL reveals a unique hydrophobic patch (W26, F87 and I237), involved in substrate binding, possibly accounting for the enzyme's high specificity. Identifying the specificity determinants will aid the development of highly specific quorum quenching enzymes as potential therapeutics.

Organizational Affiliation

Biochemistry, Molecular Biology & Biophysics Dpt and BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, 55108, USA.

Macromolecule Content

Total Structure Weight: 97.31 kDa
Atom Count: 7,292
Modeled Residue Count: 827
Deposited Residue Count: 846
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B [auth H], C [auth L]	282	Alicyclobacillus acidoterrestris ATCC 49025	Mutation(s): 0 Gene Names: N007_09425
UniProt
Find proteins for T0BMH6 (Alicyclobacillus acidoterrestris (strain ATCC 49025 / DSM 3922 / CIP 106132 / NCIMB 13137 / GD3B)) Explore T0BMH6 Go to UniProtKB: T0BMH6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	T0BMH6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth H] SDF format, chain R [auth L] MOL2 format, chain H [auth A] MOL2 format, chain N [auth H] MOL2 format, chain R [auth L] mmCIF format, chain H [auth A] mmCIF format, chain N [auth H] mmCIF format, chain R [auth L]	H [auth A], N [auth H], R [auth L]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain N [auth H] Focus chain R [auth L] Interactions & Density Focus chain H [auth A] Focus chain N [auth H] Focus chain R [auth L]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth H] MOL2 format, chain D [auth A] MOL2 format, chain I [auth H] mmCIF format, chain D [auth A] mmCIF format, chain I [auth H]	D [auth A], I [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth H] Interactions & Density Focus chain D [auth A] Focus chain I [auth H]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth H] SDF format, chain Q [auth L] SDF format, chain M [auth H] MOL2 format, chain G [auth A] MOL2 format, chain L [auth H] MOL2 format, chain Q [auth L] MOL2 format, chain M [auth H] mmCIF format, chain G [auth A] mmCIF format, chain L [auth H] mmCIF format, chain Q [auth L] mmCIF format, chain M [auth H]	G [auth A], L [auth H], M [auth H], Q [auth L]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth H] Focus chain M [auth H] Focus chain Q [auth L] Interactions & Density Focus chain G [auth A] Focus chain L [auth H] Focus chain M [auth H] Focus chain Q [auth L]
CO Query on CO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth H] SDF format, chain K [auth H] SDF format, chain O [auth L] SDF format, chain P [auth L] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth H] MOL2 format, chain K [auth H] MOL2 format, chain O [auth L] MOL2 format, chain P [auth L] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth H] mmCIF format, chain K [auth H] mmCIF format, chain O [auth L] mmCIF format, chain P [auth L]	E [auth A] F [auth A] J [auth H] K [auth H] O [auth L] E [auth A], F [auth A], J [auth H], K [auth H], O [auth L], P [auth L]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth H] Focus chain K [auth H] Focus chain O [auth L] Focus chain P [auth L] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth H] Focus chain K [auth H] Focus chain O [auth L] Focus chain P [auth L]