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 
  • R-Value Observed: 0.162 

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:  
    4YF9, 4YFA, 4YFB, 5C9I

  • 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 has acylase activity against both N-acylhomoserine lactones (AHLs), a class of signalling compounds involved in quorum sensing, and β-lactam antibiotics ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein related to penicillin acylaseA, D, G, J178Acidovorax sp. MR-S7Mutation(s): 0 
Gene Names: AVS7_00617
UniProt
Find proteins for A0A0A1VBK6 (Acidovorax sp. MR-S7)
Explore A0A0A1VBK6 
Go to UniProtKB:  A0A0A1VBK6
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein related to penicillin acylaseB, E, H, K27Acidovorax sp. MR-S7Mutation(s): 0 
Gene Names: AVS7_00617
UniProt
Find proteins for A0A0A1VBK6 (Acidovorax sp. MR-S7)
Explore A0A0A1VBK6 
Go to UniProtKB:  A0A0A1VBK6
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Protein related to penicillin acylaseC, F, I, L581Acidovorax sp. MR-S7Mutation(s): 0 
Gene Names: AVS7_00617
UniProt
Find proteins for A0A0A1VBK6 (Acidovorax sp. MR-S7)
Explore A0A0A1VBK6 
Go to UniProtKB:  A0A0A1VBK6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.472α = 90
b = 139.026β = 111.06
c = 122.001γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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