4GD8

SHV-1 beta-lactamase in complex with penam sulfone SA3-53


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of SHV-1 beta-lactamase with penem and penam sulfone inhibitors that form cyclic intermediates stabilized by carbonyl conjugation

Ke, W.Pattanaik, P.Bethel, C.R.Sheri, A.Buynak, J.D.Bonomo, R.A.van den Akker, F.

(2012) Plos One 7: e49035-e49035

  • DOI: 10.1371/journal.pone.0049035
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial β-lactamase enzymes are in large part responsible for the decreased ability of β-lactam antibiotics to combat infections. The inability to overcome β-lactamase mediated resistance spurred the development of inhibitors with penems and penam ...

    Bacterial β-lactamase enzymes are in large part responsible for the decreased ability of β-lactam antibiotics to combat infections. The inability to overcome β-lactamase mediated resistance spurred the development of inhibitors with penems and penam sulfones being amongst the most potent and broad spectrum mechanism-based inactivators. These inhibitors form covalent, "suicide-type" inhibitory intermediates that are attached to the catalytic S70 residue. To further probe the details of the mechanism of β-lactamase inhibition by these novel compounds, we determined the crystal structures of SHV-1 bound with penem 1, and penam sulfones SA1-204 and SA3-53. Comparison with each other and with previously determined crystal structures of members of these classes of inhibitors suggests that the final conformation of the covalent adduct can vary greatly amongst the complex structures. In contrast, a common theme of carbonyl conjugation as a mechanism to avoid deacylation emerges despite that the penem and penam sulfone inhibitors form different types of intermediates. The detailed insights gained from this study could be used to further improve new mechanism-based inhibitors of these common class A serine β-lactamases.


    Organizational Affiliation

    Department of Biochemistry, Case Western Reserve University, Cleveland, OH, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase SHV-1
A
286Klebsiella pneumoniaeMutation(s): 0 
Gene Names: bla (shv1)
EC: 3.5.2.6
Find proteins for P0AD64 (Klebsiella pneumoniae)
Go to UniProtKB:  P0AD64
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MA4
Query on MA4

Download SDF File 
Download CCD File 
A
CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE
C24 H44 O11
WUCWJXGMSXTDAV-QKMCSOCLSA-N
 Ligand Interaction
MXF
Query on MXF

Download SDF File 
Download CCD File 
A
(2S,3R)-4-(2-aminoethylcarbamoyloxy)-2-[(2-methanoylindolizin-3-yl)amino]-3-methyl-3-sulfino-butanoic acid
penam sulfone SA3-53, open form
C17 H22 N4 O7 S
UGXGYKKZKHIUJW-GUYCJALGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.394α = 90.00
b = 55.460β = 90.00
c = 83.649γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-08-07
    Type: Database references