6NP2

AAC-VIa bound to Sisomicin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.130 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Low-Barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of a Catalytic Triad.

Kumar, P.Agarwal, P.K.Waddell, M.B.Mittag, T.Serpersu, E.H.Cuneo, M.J.

(2019) Angew Chem Int Ed Engl 58: 16260-16266

  • DOI: https://doi.org/10.1002/anie.201908535
  • Primary Citation of Related Structures:  
    6NP1, 6NP2, 6NP3, 6NP4, 6NP5, 6NTI, 6NTJ, 6O5U

  • PubMed Abstract: 

    The position, bonding and dynamics of hydrogen atoms in the catalytic centers of proteins are essential for catalysis. The role of short hydrogen bonds in catalysis has remained highly debated and led to establishment of several distinctive geometrical arrangements of hydrogen atoms vis-à-vis the heavier donor and acceptor counterparts, that is, low-barrier, single-well or short canonical hydrogen bonds. Here we demonstrate how the position of a hydrogen atom in the catalytic triad of an aminoglycoside inactivating enzyme leads to a thirty-fold increase in catalytic turnover. A low-barrier hydrogen bond is present in the enzyme active site for the substrates that are turned over the best, whereas a canonical hydrogen bond is found with the least preferred substrate. This is the first comparison of these hydrogen bonds involving an identical catalytic network, while directly demonstrating how active site electrostatics adapt to the electronic nature of substrates to tune catalysis.


  • Organizational Affiliation

    Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminoglycoside N(3)-acetyltransferase268Enterobacter cloacaeMutation(s): 1 
Gene Names: aac 3-VI
EC: 2.3.1.81 (PDB Primary Data), 2.3.1 (UniProt)
UniProt
Find proteins for Q47030 (Enterobacter cloacae)
Explore Q47030 
Go to UniProtKB:  Q47030
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47030
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SIS
Query on SIS

Download Ideal Coordinates CCD File 
B [auth A](1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside
C19 H37 N5 O7
URWAJWIAIPFPJE-YFMIWBNJSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.130 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.304α = 90
b = 86.007β = 119.74
c = 50.164γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description