5HT0

Crystal structure of an Antibiotic_NAT family aminoglycoside acetyltransferase HMB0038 from an uncultured soil metagenomic sample in complex with coenzyme A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

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Literature

Structural and molecular rationale for the diversification of resistance mediated by the Antibiotic_NAT family.

Stogios, P.J., Bordeleau, E., Xu, Z., Skarina, T., Evdokimova, E., Chou, S., Diorio-Toth, L., D'Souza, A.W., Patel, S., Dantas, G., Wright, G.D., Savchenko, A.

(2022) Commun Biol 5: 263-263

  • DOI: https://doi.org/10.1038/s42003-022-03219-w
  • Primary Citation of Related Structures:  
    5HT0, 6MMZ, 6MN0, 6MN3, 6MN4, 6MN5, 7KES, 7LAO, 7LAP

  • PubMed Abstract: 

    • The environmental microbiome harbors a vast repertoire of antibiotic resistance genes (ARGs) which can serve as evolutionary predecessors for ARGs found in pathogenic bacteria, or can be directly mobilized to pathogens in the presence of selection pressures ...

    The environmental microbiome harbors a vast repertoire of antibiotic resistance genes (ARGs) which can serve as evolutionary predecessors for ARGs found in pathogenic bacteria, or can be directly mobilized to pathogens in the presence of selection pressures. Thus, ARGs from benign environmental bacteria are an important resource for understanding clinically relevant resistance. Here, we conduct a comprehensive functional analysis of the Antibiotic_NAT family of aminoglycoside acetyltransferases. We determined a pan-family antibiogram of 21 Antibiotic_NAT enzymes, including 8 derived from clinical isolates and 13 from environmental metagenomic samples. We find that environment-derived representatives confer high-level, broad-spectrum resistance, including against the atypical aminoglycoside apramycin, and that a metagenome-derived gene likely is ancestral to an aac(3) gene found in clinical isolates. Through crystallographic analysis, we rationalize the molecular basis for diversification of substrate specificity across the family. This work provides critical data on the molecular mechanism underpinning resistance to established and emergent aminoglycoside antibiotics and broadens our understanding of ARGs in the environment.

    Organizational Affiliation: 

    Center for Structural Genomics of Infectious Diseases (CSGID), University of Calgary, Calgary, T2N 4N1, Canada. alexei.savchenko@ucalgary.ca.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aminoglycoside acetyltransferase HMB0005
A, B, C, D, E, F
A, B, C, D, E, F
263uncultured bacteriumMutation(s): 0 
EC: 2.3.1.81
UniProt
Find proteins for A0A059X981 (uncultured bacterium)
Explore A0A059X981 
Go to UniProtKB:  A0A059X981
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A059X981
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA
Download Ideal Coordinates CCD File 
DA [auth F],
G [auth A],
L [auth B],
R [auth C],
V [auth D],
DA [auth F],
G [auth A],
L [auth B],
R [auth C],
V [auth D],
Z [auth E]
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
AA [auth E],
BA [auth E],
CA [auth E],
EA [auth F],
FA [auth F],
AA [auth E],
BA [auth E],
CA [auth E],
EA [auth F],
FA [auth F],
GA [auth F],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
S [auth C],
T [auth C],
U [auth C],
W [auth D],
X [auth D],
Y [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.016α = 90
b = 159.501β = 94.74
c = 146.225γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
BALBESphasing
PHENIXmodel building
Cootmodel building

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: 2022-04-06
    Changes: Database references, Derived calculations