2H5S | pdb_00002h5s

SA2-13 penam sulfone complexed to wt SHV-1 beta-lactamase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 
    0.167 (Depositor), 0.160 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.154 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MA4Click on this verticalbar to view detailsBest fitted SA2Click on this verticalbar to view details

This is version 1.5 of the entry. See complete history


Literature

Rational Design of a beta-Lactamase Inhibitor Achieved via Stabilization of the trans-Enamine Intermediate: 1.28 A Crystal Structure of wt SHV-1 Complex with a Penam Sulfone.

Padayatti, P.S.Sheri, A.Totir, M.A.Helfand, M.S.Carey, M.P.Anderson, V.E.Carey, P.R.Bethel, C.R.Bonomo, R.A.Buynak, J.D.van den Akker, F.

(2006) J Am Chem Soc 128: 13235-13242

  • DOI: https://doi.org/10.1021/ja063715w
  • Primary Citation of Related Structures:  
    2H5S

  • PubMed Abstract: 

    beta-Lactamases are one of the major causes of antibiotic resistance in Gram negative bacteria. The continuing evolution of beta-lactamases that are capable of hydrolyzing our most potent beta-lactams presents a vexing clinical problem, in particular since a number of them are resistant to inhibitors. The efficient inhibition of these enzymes is therefore of great clinical importance. Building upon our previous structural studies that examined tazobactam trapped as a trans-enamine intermediate in a deacylation deficient SHV variant, we designed a novel penam sulfone derivative that forms a more stable trans-enamine intermediate. We report here the 1.28 A resolution crystal structure of wt SHV-1 in complex with a rationally designed penam sulfone, SA2-13. The compound is covalently bound to the active site of wt SHV-1 similar to tazobactam yet forms an additional salt-bridge with K234 and hydrogen bonds with S130 and T235 to stabilize the trans-enamine intermediate. Kinetic measurements show that SA2-13, once reacted with SHV-1 beta-lactamase, is about 10-fold slower at being released from the enzyme compared to tazobactam. Stabilizing the trans-enamine intermediate represents a novel strategy for the rational design of mechanism-based class A beta-lactamase inhibitors.


  • Organizational Affiliation

    Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SHV-1 beta-lactamase265Klebsiella pneumoniaeMutation(s): 0 
EC: 3.5.2.6
UniProt
Find proteins for P0AD64 (Klebsiella pneumoniae)
Explore P0AD64 
Go to UniProtKB:  P0AD64
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AD64
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free:  0.167 (Depositor), 0.160 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.154 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.81α = 90
b = 55.22β = 90
c = 84.43γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MA4Click on this verticalbar to view detailsBest fitted SA2Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-13
    Changes: Structure summary