6MN0 | pdb_00006mn0

Crystal structure of meta-AAC0038, an environmental aminoglycoside resistance enzyme, H168A mutant in complex with acetyl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.208 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

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 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. 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
    • Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, M5S 3E5, Canada.

Macromolecule Content 

  • Total Structure Weight: 184.45 kDa 
  • Atom Count: 14,281 
  • Modeled Residue Count: 1,562 
  • Deposited Residue Count: 1,578 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Aminoglycoside N(3)-acetyltransferase
A, B, C, D, E
A, B, C, D, E, F
263uncultured bacteriumMutation(s): 1 
EC: 2.3.1.81
UniProt
Find proteins for A0ACD6B8R8 (uncultured bacterium)
Explore A0ACD6B8R8 
Go to UniProtKB:  A0ACD6B8R8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B8R8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACO

Query on ACO



Download:Ideal Coordinates CCD File
BA [auth D]
G [auth A]
HA [auth E]
P [auth B]
QA [auth F]
BA [auth D],
G [auth A],
HA [auth E],
P [auth B],
QA [auth F],
U [auth C]
ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
PE3

Query on PE3



Download:Ideal Coordinates CCD File
AA [auth C]
M [auth A]
N [auth A]
O [auth A]
PA [auth E]
AA [auth C],
M [auth A],
N [auth A],
O [auth A],
PA [auth E],
S [auth B],
T [auth B],
WA [auth F]
3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
C28 H58 O15
ILLKMACMBHTSHP-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
FA [auth D]
GA [auth D]
J [auth A]
JA [auth E]
K [auth A]
FA [auth D],
GA [auth D],
J [auth A],
JA [auth E],
K [auth A],
KA [auth E],
L [auth A],
LA [auth E],
MA [auth E],
NA [auth E],
OA [auth E],
Q [auth B],
R [auth B],
SA [auth F],
TA [auth F],
UA [auth F],
VA [auth F],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
CA [auth D],
DA [auth D],
EA [auth D],
I [auth A],
IA [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
H [auth A],
RA [auth F],
V [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.208 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.078α = 90
b = 159.62β = 94.56
c = 143.321γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700060C

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2022-04-06
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Refinement description