6RFX

Crystal structure of Eis2 from Mycobacterium abscessus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the aminoglycosides N-acetyltransferase Eis2 from Mycobacterium abscessus.

Ung, K.L.Alsarraf, H.M.A.B.Olieric, V.Kremer, L.Blaise, M.

(2019) FEBS J 286: 4342-4355

  • DOI: https://doi.org/10.1111/febs.14975
  • Primary Citation of Related Structures:  
    6RFT, 6RFX, 6RFY

  • PubMed Abstract: 

    Mycobacterium abscessus is an emerging human pathogen that is notorious for being one of the most drug-resistant species of Mycobacterium. It has developed numerous strategies to overcome the antibiotic stress response, limiting treatment options and leading to frequent therapeutic failure. The panel of aminoglycosides (AG) usually used in the treatment of M. abscessus pulmonary infections is restricted by chemical modification of the drugs by the N-acetyltransferase Eis2 protein (Mabs_Eis2). This enzyme acetylates the primary amine of AGs, preventing these antibiotics from binding ribosomal RNA and thereby impairing their activity. In this study, the high-resolution crystal structures of Mabs_Eis2 in its apo- and cofactor-bound forms were solved. The structural analysis of Mabs_Eis2, supported by the kinetic characterization of the enzyme, highlights the large substrate specificity of the enzyme. Furthermore, in silico docking and biochemical approaches attest that Mabs_Eis2 modifies clinically relevant drugs such as kanamycin and amikacin, with a better efficacy for the latter. In line with previous biochemical and in vivo studies, our work suggests that Mabs_Eis2 represents an attractive pharmacological target to be further explored. The high-resolution crystal structures presented here may pave the way to the design of Eis2-specific inhibitors with the potential to counteract the intrinsic resistance levels of M. abscessus to an important class of clinically important antibiotics. DATABASE: Structural data are available in the PDB database under the accession numbers: 6RFY, 6RFX and 6RFT.


  • Organizational Affiliation

    Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eis2411Mycobacteroides abscessusMutation(s): 0 
Gene Names: D2E36_21790
EC: 2.3.1
UniProt
Find proteins for A0A1M9A4M7 (Mycobacteroides abscessus subsp. abscessus)
Explore A0A1M9A4M7 
Go to UniProtKB:  A0A1M9A4M7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1M9A4M7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P4K
Query on P4K

Download Ideal Coordinates CCD File 
H [auth D]
K [auth A]
M [auth A]
O [auth B]
Q [auth B]
H [auth D],
K [auth A],
M [auth A],
O [auth B],
Q [auth B],
S [auth C],
V [auth E]
polyethylene glycol
C30 H62 O15
WWPGFZAAWXFBTF-UHFFFAOYSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
G [auth D]
J [auth A]
N [auth B]
R [auth C]
U [auth E]
G [auth D],
J [auth A],
N [auth B],
R [auth C],
U [auth E],
X [auth F]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
I [auth D],
L [auth A],
P [auth B],
T [auth C],
W [auth E]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A [auth D]
B [auth A]
C [auth B]
D [auth C]
E
A [auth D],
B [auth A],
C [auth B],
D [auth C],
E,
F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.45α = 90
b = 79.8β = 90.29
c = 152.68γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
AutoSolphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Database references