4G8B | pdb_00004g8b

Crystal structures of N-acyl homoserine lactonase AidH S102G mutant complexed with N-hexanoyl homoserine lactone

• PDB DOI: https://doi.org/10.2210/pdb4G8B/pdb

• Classification: HYDROLASE
• Organism(s): Ochrobactrum sp. T63
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-07-23 Released: 2013-01-16 
• Deposition Author(s): Liang, D.C., Yan, X.X., Gao, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.159 (Depositor), 0.126 (DCC) 
• R-Value Work: 
  0.122 (Depositor), 0.126 (DCC) 
• R-Value Observed: 
  0.124 (Depositor) 

Starting Model: experimental

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 D Biol Crystallogr 69: 82-91

• PubMed: 23275166 
• DOI: https://doi.org/10.1107/S0907444912042369
• Primary Citation Related Structures: 
  4G5X, 4G8B, 4G8C, 4G8D, 4G9E, 4G9G


• 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 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.

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

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 61.65 kDa 
• Atom Count: 5,317 
• Modeled Residue Count: 548 
• Deposited Residue Count: 558 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha/beta hydrolase fold protein	A, B	279	Ochrobactrum sp. T63	Mutation(s): 1  Gene Names: aidH
UniProt
Find proteins for D2J2T6 (Ochrobactrum sp. T63) Explore D2J2T6  Go to UniProtKB:  D2J2T6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HL6	C [auth A], D [auth B]	N-[(3S)-2-oxotetrahydrofuran-3-yl]hexanamide C10 H17 N O3 ZJFKKPDLNLCPNP-QMMMGPOBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.159 (Depositor), 0.126 (DCC) 
• R-Value Work:  0.122 (Depositor), 0.126 (DCC) 
• R-Value Observed: 0.124 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.385	α = 90
b = 130.075	β = 110.68
c = 44.254	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-16 
Deposition Author(s): Liang, D.C., Yan, X.X., Gao, A.

Revision History  

• Version 1.0: 2013-01-16
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description