6SUL

Amicoumacin kinase AmiN in complex with AMP-PNP, Mg2+ and Ami


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 

wwPDB Validation   3D Report Full Report


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
Phosphotransferase enzyme family protein, amicoumacin kinase
A, B, C, D
335Bacillus pumilusMutation(s): 0 
Gene Names: C6X97_15155EJB14_06995
EC: 2.7.1.230
UniProt
Find proteins for A8FAR5 (Bacillus pumilus (strain SAFR-032))
Explore A8FAR5 
Go to UniProtKB:  A8FAR5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8FAR5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
DA [auth D],
K [auth A],
Q [auth B],
W [auth C]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
UAM
Query on UAM

Download Ideal Coordinates CCD File 
CA [auth D],
J [auth A],
P [auth B],
V [auth C]
Amicoumacin A
C20 H29 N3 O7
DCPWYLSPIAHJFU-YKRRISCLSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
G [auth A]
H [auth A]
I [auth A]
AA [auth D],
BA [auth D],
G [auth A],
H [auth A],
I [auth A],
N [auth B],
O [auth B],
T [auth C],
U [auth C],
Z [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
L [auth B]
M [auth B]
R [auth C]
E [auth A],
F [auth A],
L [auth B],
M [auth B],
R [auth C],
S [auth C],
X [auth D],
Y [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.34α = 89.95
b = 76.77β = 99.62
c = 101.2γ = 91.44
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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