4YFB

Structure of N-acylhomoserine lactone acylase MacQ in complex with phenylacetic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Bifunctional quorum-quenching and antibiotic-acylase MacQ forms a 170-kDa capsule-shaped molecule containing spacer polypeptides

Yasutake, Y.Kusada, H.Ebuchi, T.Hanada, S.Kamagata, Y.Tamura, T.Kimura, N.

(2017) Sci Rep 7: 8946-8946

  • DOI: 10.1038/s41598-017-09399-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Understanding the molecular mechanisms of bacterial antibiotic resistance will help prepare against further emergence of multi-drug resistant strains. MacQ is an enzyme responsible for the multi-drug resistance of Acidovorax sp. strain MR-S7. MacQ ha ...

    Understanding the molecular mechanisms of bacterial antibiotic resistance will help prepare against further emergence of multi-drug resistant strains. MacQ is an enzyme responsible for the multi-drug resistance of Acidovorax sp. strain MR-S7. MacQ has acylase activity against both N-acylhomoserine lactones (AHLs), a class of signalling compounds involved in quorum sensing, and β-lactam antibiotics. Thus, MacQ is crucial as a quencher of quorum sensing as well as in conferring antibiotic resistance in Acidovorax. Here, we report the X-ray structures of MacQ in ligand-free and reaction product complexes. MacQ forms a 170-kDa capsule-shaped molecule via face-to-face interaction with two heterodimers consisting of an α-chain and a β-chain, generated by the self-cleaving activity of a precursor polypeptide. The electron density of the spacer polypeptide in the hollow of the molecule revealed the close orientation of the peptide-bond atoms of Val20SP-Gly21SP to the active-site, implying a role of the residues in substrate binding. In mutational analyses, uncleaved MacQ retained degradation activity against both AHLs and penicillin G. These results provide novel insights into the mechanism of self-cleaving maturation and enzymatic function of N-terminal nucleophile hydrolases.


    Organizational Affiliation

    Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki, 305-8572, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo, 062-8517, Japan. y-yasutake@aist.go.jp.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo, 062-8517, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein related to penicillin acylase
A, D, G, J
178Acidovorax sp. MR-S7Mutation(s): 0 
Find proteins for A0A0A1VBK6 (Acidovorax sp. MR-S7)
Go to UniProtKB:  A0A0A1VBK6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein related to penicillin acylase
B, E, H, K
27Acidovorax sp. MR-S7Mutation(s): 0 
Find proteins for A0A0A1VBK6 (Acidovorax sp. MR-S7)
Go to UniProtKB:  A0A0A1VBK6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein related to penicillin acylase
C, F, I, L
581Acidovorax sp. MR-S7Mutation(s): 0 
Find proteins for A0A0A1VBK6 (Acidovorax sp. MR-S7)
Go to UniProtKB:  A0A0A1VBK6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAC
Query on PAC

Download SDF File 
Download CCD File 
C, F, I, L
2-PHENYLACETIC ACID
C8 H8 O2
WLJVXDMOQOGPHL-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
C, F, I, L
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 102.472α = 90.00
b = 139.026β = 111.06
c = 122.001γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Data collection, Database references, Derived calculations