6NTI

Neutron/X-ray crystal structure of AAC-VIa bound to kanamycin b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 

  • Method: NEUTRON DIFFRACTION

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 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 ...

    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

    Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aminoglycoside N(3)-acetyltransferaseA302EnterobacteriaceaeMutation(s): 0 
Gene Names: aacCaac3-VIaac3-VI_1NCTC13462_00209pAPEC1990_61_126pAR060302_0140pAR060302_133peH4H_0115SAMEA3485113_05325
EC: 2.3.1.81
UniProt
Find proteins for C4NV15 (Escherichia coli)
Explore C4NV15 
Go to UniProtKB:  C4NV15
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4NV15
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9CS
Query on 9CS

Download Ideal Coordinates CCD File 
B [auth A](1R,2S,3S,4R,6S)-4,6-DIAMINO-3-[(3-AMINO-3-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-HYDROXYCYCLOHEXYL 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSIDE
C18 H37 N5 O10
SKKLOUVUUNMCJE-FQSMHNGLSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 
  • Space Group: I 1 2 1
  • Method: NEUTRON DIFFRACTION
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.359α = 90
b = 86.058β = 93.98
c = 77.597γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2019-01-29 
  • Released Date: 2019-09-25 
  • Deposition Author(s): Cuneo, M.J., Kumar, P.

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