Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 107.26 kDa 
• Atom Count: 7868 
• Modelled Residue Count: 828 
• Deposited Residue Count: 891 
• Unique protein chains: 1

6N9R

Structure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus bound to substrate 3-oxo-C12-AHL

• DOI: 10.2210/pdb6N9R/pdb

• Classification: HYDROLASE
• Organism(s): Parageobacillus caldoxylosilyticus NBRC 107762
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-12-03 Released: 2019-04-03 
• Deposition Author(s): Bergonzi, C., Schwab, M., Elias, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.235 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 

Literature

The Structural Determinants Accounting for the Broad Substrate Specificity of the Quorum Quenching Lactonase GcL.

Bergonzi, C., Schwab, M., Naik, T., Elias, M.

(2019) Chembiochem 20: 1848-1855

• PubMed: 30864300 
• DOI: 10.1002/cbic.201900024
• Primary Citation of Related Structures:  
  6N9I, 6N9Q, 6N9R


• PubMed Abstract: 
  

Quorum quenching lactonases are enzymes capable of hydrolyzing lactones, including N-acyl homoserine lactones (AHLs). AHLs are molecules known as signals in bacterial communication dubbed quorum sensing. Bacterial signal disruption by lactonases was previously reported to inhibit behavior regulated by quorum sensing, such as the expression of virulence factors and the formation of biofilms. Herein, we report the enzymatic and structural characterization of a novel lactonase representative from the metallo-β-lactamase superfamily, dubbed GcL. GcL is a broad spectrum and highly proficient lactonase, with k _cat /K _M values in the range of 10 ⁴ to 10 ⁶  m ^-1  s ^-1 . Analysis of free GcL structures and in complex with AHL substrates of different acyl chain length, namely, C4-AHL and 3-oxo-C12-AHL, allowed their respective binding modes to be elucidated. Structures reveal three subsites in the binding crevice: 1) the small subsite where chemistry is performed on the lactone ring; 2) a hydrophobic ring that accommodates the amide group of AHLs and small acyl chains; and 3) the outer, hydrophilic subsite that extends to the protein surface. Unexpectedly, the absence of structural accommodation for long substrate acyl chains seems to relate to the broad substrate specificity of the enzyme.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative hydrolase	A, B [auth P], C [auth X]	297	Parageobacillus caldoxylosilyticus NBRC 107762	Mutation(s): 0  Gene Names: GCA01S_030_00190
UniProt
Find proteins for A0A023DFE8 (Parageobacillus caldoxylosilyticus NBRC 107762) Explore A0A023DFE8  Go to UniProtKB:  A0A023DFE8

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OHN (Subject of Investigation/LOI)	F [auth A], JA [auth X], X [auth P]	N-3-OXO-DODECANOYL-L-HOMOSERINE LACTONE C16 H27 N O4 PHSRRHGYXQCRPU-AWEZNQCLSA-N
1PE	EA [auth P], O [auth A], SA [auth X]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PGE	P [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4	HA [auth X], IA [auth X], S [auth P], T [auth P], U [auth P], V [auth P], W [auth P]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	AA [auth P], BA [auth P], CA [auth P], DA [auth P], J [auth A], K [auth A], L [auth A], LA [auth X], M [auth A], MA [auth X], N [auth A], NA [auth X], OA [auth X], PA [auth X], QA [auth X], RA [auth X], Z [auth P]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	G [auth A], H [auth A], I [auth A], KA [auth X], Y [auth P]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CO	D [auth A], FA [auth X], Q [auth P]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
FE	E [auth A], GA [auth X], R [auth P]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.235 
• R-Value Work: 0.176 
• R-Value Observed: 0.179 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.01	α = 90
b = 108.59	β = 115.75
c = 78.6	γ = 90

Software Package:

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

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2018-12-03 
• Released Date: 2019-04-03 
Deposition Author(s): Bergonzi, C., Schwab, M., Elias, M.

Revision History  

• Version 1.0: 2019-04-03
  Type: Initial release
  
• Version 1.1: 2019-08-14
  Changes: Data collection, Database references