11TV | pdb_000011tv

Crystal structure of alpha/beta-hydrolase macrolide esterase EstX from Escherichia coli (S102A mutant) in complex with linearized tylosin

• PDB DOI: https://doi.org/10.2210/pdb11TV/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2026-03-12 Released: 2026-04-08 
• Deposition Author(s): Kelly, E.T.R., Blanchet, J., Berghuis, A.M.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.199 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: in silico

Literature

Hydration and hydrolysis define antibiotic resistance conferred by macrolide esterases.

Kelly, E.T.R., Myziuk, I., Hemmings, M.Z., Mulla, Z., Blanchet, J., Ruzzini, A., Berghuis, A.M.

(2026) Proc Natl Acad Sci U S A 123: e2611077123-e2611077123

• PubMed: 42455676 
• DOI: https://doi.org/10.1073/pnas.2611077123
• Primary Citation Related Structures: 
  11TS, 11TT, 11TU, 11TV, 11TW


• PubMed Abstract: 
  

  Macrolides are an antibiotic class widely used in both human and veterinary medicine, and function by interfering with protein synthesis. Regrettably, numerous strategies for evading the antibiotic properties of macrolides have been found in bacteria, including enzyme-mediated inactivation. These mechanisms are now widely disseminated among pathogenic, animal-associated, and environmental bacteria making them a One Health issue. Macrolide esterases, which hydrolyze the macrolactone's ester bond, confer one such resistance mechanism. Two types of macrolide esterases have thus far been identified, the well-studied erythromycin esterases and the recently discovered Est-type enzymes that belong to the α/β-hydrolase superfamily. We present detailed structure-function studies for four diverse Est type esterases: which only share 44 to 66% sequence identity (EstT _Sf , EstT _St , EstT _Bc , and EstX _Ec ). In addition to resistance profiling and substrate specificity studies, we present structures for all four enzymes, including structures for EstT _Bc and EstX _Ec in complex with tylosin and tylvalosin macrolides, posthydrolysis. Complementing the data with mutational and kinetic studies allowed for a detailed analysis of the structural basis for macrolide-enzyme interactions. Combined, the data suggest that promiscuous binding and imprecise positioning, mediated by a water-cage, dictate substrate specificity for Est-type macrolide resistance enzymes. These insights may prove beneficial for next-generation antibiotic development.

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Organizational Affiliation: 
• Department of Biochemistry, McGill University, Montréal, QC H3A 1A3, Canada.
Centre de recherche en biologie structurale, McGill University, Montréal, QC H3G 0B1, Canada.
McGill Antimicrobial Resistance Center, Montréal, QC H4A 0B1, Canada.
Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada.
Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 63.98 kDa 
• Atom Count: 4,765 
• Modeled Residue Count: 559 
• Deposited Residue Count: 560 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha/beta-hydrolase macrolide esterase EstX	A [auth D], B [auth A]	280	Escherichia coli	Mutation(s): 1  Gene Names: estX, rdmC, sat
UniProt
Find proteins for Q75WM3 (Escherichia coli) Explore Q75WM3  Go to UniProtKB:  Q75WM3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1E2O (Subject of Investigation/LOI)	C [auth D], D [auth A]	(3~{R},4~{S},5~{S},6~{R},8~{R},10~{E},12~{E},14~{R},15~{R})-14-[[(2~{R},3~{R},4~{R},5~{R},6~{R})-3,4-dimethoxy-6-methyl-5-oxidanyl-oxan-2-yl]oxymethyl]-5-[(2~{R},3~{R},4~{R},5~{S},6~{R})-4-(dimethylamino)-5-[(2~{S},4~{R},5~{S},6~{S})-4,6-dimethyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-methyl-3-oxidanyl-oxan-2-yl]oxy-4,8,12-trimethyl-3,15-bis(oxidanyl)-9-oxidanylidene-6-(2-oxidanylideneethyl)heptadeca-10,12-dienoic acid C46 H79 N O18 LABOOMGUZLDCMV-WBBQIANUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.199 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.594	α = 90
b = 72.691	β = 95.73
c = 82.051	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-08 
Deposition Author(s): Kelly, E.T.R., Blanchet, J., Berghuis, A.M.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	PJT-162365

Revision History  

• Version 1.0: 2026-04-08
  Type: Initial release
  
• Version 1.1: 2026-07-29
  Changes: Database references