7MQM | pdb_00007mqm

AAC(3)-IIIa in complex with CoA and gentamicin

PDB DOI: https://doi.org/10.2210/pdb7MQM/pdb

Classification: TRANSFERASE
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-05-05 Released: 2022-07-06
Deposition Author(s): Zielinski, M., Berghuis, A.M.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.216 (Depositor), 0.215 (DCC)
R-Value Work:
0.197 (Depositor), 0.194 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural elucidation of substrate-bound aminoglycoside acetyltransferase (3)-IIIa.

Zielinski, M., Blanchet, J., Hailemariam, S., Berghuis, A.M.

(2022) PLoS One 17: e0269684-e0269684

PubMed: 35921328 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0269684
Primary Citation Related Structures:
7MQK, 7MQL, 7MQM

PubMed Abstract:
Canonical aminoglycosides are a large group of antibiotics, where the part of chemical diversity stems from the substitution of the neamine ring system on positions 5 and 6. Certain aminoglycoside modifying enzymes can modify a broad range of 4,5- and 4,6-disubstituted aminoglycosides, with some as many as 15. This study presents the structural and kinetic results describing a promiscuous aminoglycoside acetyltransferase AAC(3)-IIIa. This enzyme has been crystallized in ternary complex with coenzyme A and 4,5- and 4,6-disubstituted aminoglycosides. We have followed up this work with kinetic characterization utilizing a panel of diverse aminoglycosides, including a next-generation aminoglycoside, plazomicin. Lastly, we observed an alternative binding mode of gentamicin in the aminoglycoside binding site, which was proven to be a crystallographic artifact based on mutagenesis.

Organizational Affiliation

Department of Biochemistry, McGill University, Montréal, Québec, Canada.

Macromolecule Content

Total Structure Weight: 124.96 kDa
Atom Count: 9,900
Modeled Residue Count: 1,043
Deposited Residue Count: 1,096
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminoglycoside N(3)-acetyltransferase III	A, B, C, D	274	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: aacC3 EC: 2.3.1.81
UniProt
Find proteins for P29808 (Pseudomonas aeruginosa) Explore P29808 Go to UniProtKB: P29808
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29808
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA (Subject of Investigation/LOI) Query on COA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	E [auth A], H [auth B], K [auth C], M [auth D]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D]
51G (Subject of Investigation/LOI) Query on 51G Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B], L [auth C], N [auth D]	gentamicin C1 C₂₁ H₄₃ N₅ O₇ CEAZRRDELHUEMR-CAMVTXANSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B]	G [auth A], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth B]