6N9R

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


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 

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Ligand Structure Quality Assessment 


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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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative hydrolaseA, B [auth P], C [auth X]297Parageobacillus caldoxylosilyticus NBRC 107762Mutation(s): 0 
Gene Names: GCA01S_030_00190
UniProt
Find proteins for A0A023DFE8 (Parageobacillus caldoxylosilyticus NBRC 107762)
Explore A0A023DFE8 
Go to UniProtKB:  A0A023DFE8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OHN (Subject of Investigation/LOI)
Query on OHN

Download Ideal Coordinates CCD File 
F [auth A], JA [auth X], X [auth P]N-3-OXO-DODECANOYL-L-HOMOSERINE LACTONE
C16 H27 N O4
PHSRRHGYXQCRPU-AWEZNQCLSA-N
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
EA [auth P], O [auth A], SA [auth X]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
P [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth P] , BA [auth P] , CA [auth P] , DA [auth P] , J [auth A] , K [auth A] , L [auth A] , LA [auth X] , 
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
 Ligand Interaction
ACT
Query on ACT

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G [auth A], H [auth A], I [auth A], KA [auth X], Y [auth P]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CO
Query on CO

Download Ideal Coordinates CCD File 
D [auth A], FA [auth X], Q [auth P]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
E [auth A], GA [auth X], R [auth P]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
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 = 145.01α = 90
b = 108.59β = 115.75
c = 78.6γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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