6SUM

Amicoumacin kinase hAmiN in complex with AMP-PNP, MG2+ and Ami


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A kinase bioscavenger provides antibiotic resistance by extremely tight substrate binding.

Terekhov, S.S.Mokrushina, Y.A.Nazarov, A.S.Zlobin, A.Zalevsky, A.Bourenkov, G.Golovin, A.Belogurov Jr., A.Osterman, I.A.Kulikova, A.A.Mitkevich, V.A.Lou, H.J.Turk, B.E.Wilmanns, M.Smirnov, I.V.Altman, S.Gabibov, A.G.

(2020) Sci Adv 6: eaaz9861-eaaz9861

  • DOI: https://doi.org/10.1126/sciadv.aaz9861
  • Primary Citation of Related Structures:  
    6SUI, 6SUL, 6SUM, 6SUN, 6SV5

  • PubMed Abstract: 

    Microbial communities are self-controlled by repertoires of lethal agents, the antibiotics. In their turn, these antibiotics are regulated by bioscavengers that are selected in the course of evolution. Kinase-mediated phosphorylation represents one of the general strategies for the emergence of antibiotic resistance. A new subfamily of AmiN-like kinases, isolated from the Siberian bear microbiome, inactivates antibiotic amicoumacin by phosphorylation. The nanomolar substrate affinity defines AmiN as a phosphotransferase with a unique catalytic efficiency proximal to the diffusion limit. Crystallographic analysis and multiscale simulations revealed a catalytically perfect mechanism providing phosphorylation exclusively in the case of a closed active site that counteracts substrate promiscuity. AmiN kinase is a member of the previously unknown subfamily representing the first evidence of a specialized phosphotransferase bioscavenger.


  • Organizational Affiliation

    Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AMICOUMACIN KINASE
A, B
335Bacillus altitudinisMutation(s): 0 
Gene Names: BW16_03450
EC: 2.7.1.230
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
UAM
Query on UAM

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
Amicoumacin A
C20 H29 N3 O7
DCPWYLSPIAHJFU-YKRRISCLSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
G [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth B],
I [auth B],
L [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.66α = 112.29
b = 66β = 102.81
c = 70.41γ = 94.79
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation19-14-00331
Russian Foundation for Basic ResearchRussian Federation19-34-70021
Russian Foundation for Basic ResearchRussian Federation18-29-08054

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Data collection, Database references, Derived calculations