Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.90 kDa 
• Atom Count: 5333 
• Modelled Residue Count: 588 
• Deposited Residue Count: 588 
• Unique protein chains: 1

4ZO3

AidC, a Dizinc Quorum-Quenching Lactonase, in complex with a product N-hexnoyl-L-homoserine

• PDB DOI: 10.2210/pdb4ZO3/pdb

• Classification: HYDROLASE
• Organism(s): Chryseobacterium sp. StRB126
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-05 Released: 2015-07-15 
• Deposition Author(s): Mascarenhas, R., Thomas, P.W., Wu, C.-X., Nocek, B.P., Hoang, Q., Fast, W., Liu, D.
• Funding Organization(s): National Science Foundation (NSF, United States), Robert A. Welch Foundation, Loyola University Chicago

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.228 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

Structural and Biochemical Characterization of AidC, a Quorum-Quenching Lactonase with Atypical Selectivity.

Mascarenhas, R., Thomas, P.W., Wu, C.X., Nocek, B.P., Hoang, Q.Q., Liu, D., Fast, W.

(2015) Biochemistry 54: 4342-4353

• PubMed: 26115006 
• DOI: 10.1021/acs.biochem.5b00499
• Primary Citation of Related Structures:  
  4ZO2, 4ZO3


• PubMed Abstract: 
  

Quorum-quenching catalysts are of interest for potential application as biochemical tools for interrogating interbacterial communication pathways, as antibiofouling agents, and as anti-infective agents in plants and animals. Herein, the structure and function of AidC, an N-acyl-l-homoserine lactone (AHL) lactonase from Chryseobacterium, is characterized. Steady-state kinetics show that zinc-supplemented AidC is the most efficient wild-type quorum-quenching enzymes characterized to date, with a kcat/KM value of approximately 2 × 10(6) M(-1) s(-1) for N-heptanoyl-l-homoserine lactone. The enzyme has stricter substrate selectivity and significantly lower KM values (ca. 50 μM for preferred substrates) compared to those of typical AHL lactonases (ca. >1 mM). X-ray crystal structures of AidC alone and with the product N-hexanoyl-l-homoserine were determined at resolutions of 1.09 and 1.67 Å, respectively. Each structure displays as a dimer, and dimeric oligiomerization was also observed in solution by size-exclusion chromatography coupled with multiangle light scattering. The structures reveal two atypical features as compared to previously characterized AHL lactonases: a "kinked" α-helix that forms part of a closed binding pocket that provides affinity and enforces selectivity for AHL substrates and an active-site His substitution that is usually found in a homologous family of phosphodiesterases. Implications for the catalytic mechanism of AHL lactonases are discussed.

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Organizational Affiliation: 

§Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acylhomoserine lactonase	A, B	294	Chryseobacterium sp. StRB126	Mutation(s): 0  Gene Names: aidC, CHSO_3121
UniProt
Find proteins for I7HB71 (Chryseobacterium sp. StRB126) Explore I7HB71  Go to UniProtKB:  I7HB71

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C6L	E [auth A], H [auth B]	N-hexanoyl-L-homoserine C10 H19 N O4 BJLILZXVIKTHKQ-QMMMGPOBSA-N
ZN	C [auth A], D [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.228 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.09	α = 90
b = 47.87	β = 90
c = 249.15	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-05-05 
• Released Date: 2015-07-15 
Deposition Author(s): Mascarenhas, R., Thomas, P.W., Wu, C.-X., Nocek, B.P., Hoang, Q., Fast, W., Liu, D.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-1308672
Robert A. Welch Foundation	United States	F-1572
Loyola University Chicago	United States	--

Revision History  

• Version 1.0: 2015-07-15
  Type: Initial release
  
• Version 1.1: 2015-07-29
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
• Version 1.3: 2017-11-22
  Changes: Refinement description
• Version 1.4: 2019-11-27
  Changes: Author supporting evidence