4G9E

Crystal structures of N-acyl homoserine lactonase AidH complexed with N-butanoyl homoserine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.088 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.127 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

High-resolution structures of AidH complexes provide insights into a novel catalytic mechanism for N-acyl homoserine lactonase

Gao, A.Mei, G.Y.Liu, S.Wang, P.Tang, Q.Liu, Y.P.Wen, H.An, X.M.Zhang, L.Q.Yan, X.X.Liang, D.C.

(2013) Acta Crystallogr.,Sect.D 69: 82-91

  • DOI: 10.1107/S0907444912042369
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Many pathogenic bacteria that infect humans, animals and plants rely on a quorum-sensing (QS) system to produce virulence factors. N-Acyl homoserine lactones (AHLs) are the best-characterized cell-cell communication signals in QS. The concentration o ...

    Many pathogenic bacteria that infect humans, animals and plants rely on a quorum-sensing (QS) system to produce virulence factors. N-Acyl homoserine lactones (AHLs) are the best-characterized cell-cell communication signals in QS. The concentration of AHL plays a key role in regulating the virulence-gene expression and essential biological functions of pathogenic bacteria. N-Acyl homoserine lactonases (AHL-lactonases) have important functions in decreasing pathogenicity by degrading AHLs. Here, structures of the AHL-lactonase from Ochrobactrum sp. (AidH) in complex with N-hexanoyl homoserine lactone, N-hexanoyl homoserine and N-butanoyl homoserine are reported. The high-resolution structures together with biochemical analyses reveal convincing details of AHL degradation. No metal ion is bound in the active site, which is different from other AHL-lactonases, which have a dual Lewis acid catalysis mechanism. AidH contains a substrate-binding tunnel between the core domain and the cap domain. The conformation of the tunnel entrance varies with the AHL acyl-chain length, which contributes to the binding promiscuity of AHL molecules in the active site. It also supports the biochemical result that AidH is a broad catalytic spectrum AHL-lactonase. Taken together, the present results reveal the catalytic mechanism of the metal-independent AHL-lactonase, which is a typical acid-base covalent catalysis.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha/beta hydrolase fold protein
A, B
279Ochrobactrum sp. T63Gene Names: aidH
Find proteins for D2J2T6 (Ochrobactrum sp. T63)
Go to UniProtKB:  D2J2T6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C4L
Query on C4L

Download SDF File 
Download CCD File 
A, B
N-butanoyl-L-homoserine
C8 H15 N O4
FWULQXYJOANGSS-LURJTMIESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.088 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.127 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.164α = 90.00
b = 129.523β = 111.00
c = 44.312γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXrefinement
PHENIXphasing
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release