4MBH

Penam sulfone PSR-3-226 bound to E166A variant of SHV-1 beta-lactamase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Penam sulfones and beta-lactamase inhibition: SA2-13 and the importance of the C2 side chain length and composition.

Rodkey, E.A.Winkler, M.L.Bethel, C.R.Pagadala, S.R.Buynak, J.D.Bonomo, R.A.van den Akker, F.

(2014) PLoS One 9: e85892-e85892

  • DOI: 10.1371/journal.pone.0085892
  • Primary Citation of Related Structures:  
    4MBF, 4MBH, 4MBK

  • PubMed Abstract: 
  • β-Lactamases are the major reason β-lactam resistance is seen in Gram-negative bacteria. To combat this resistance mechanism, β-lactamase inhibitors are currently being developed. Presently, there are only three that are in clinical use (clavulanate, sul ...

    β-Lactamases are the major reason β-lactam resistance is seen in Gram-negative bacteria. To combat this resistance mechanism, β-lactamase inhibitors are currently being developed. Presently, there are only three that are in clinical use (clavulanate, sulbactam and tazobactam). In order to address this important medical need, we explored a new inhibition strategy that takes advantage of a long-lived inhibitory trans-enamine intermediate. SA2-13 was previously synthesized and shown to have a lower k(react) than tazobactam. We investigated here the importance of the carboxyl linker length and composition by synthesizing three analogs of SA2-13 (PSR-4-157, PSR-4-155, and PSR-3-226). All SA2-13 analogs yielded higher turnover numbers and k(react) compared to SA2-13. We next demonstrated using protein crystallography that increasing the linker length by one carbon allowed for better capture of a trans-enamine intermediate; in contrast, this trans-enamine intermediate did not occur when the C2 linker length was decreased by one carbon. If the linker was altered by both shortening it and changing the carboxyl moiety into a neutral amide moiety, the stable trans-enamine intermediate in wt SHV-1 did not form; this intermediate could only be observed when a deacylation deficient E166A variant was studied. We subsequently studied SA2-13 against a relatively recently discovered inhibitor-resistant (IR) variant of SHV-1, SHV K234R. Despite the alteration in the mechanism of resistance due to the K→R change in this variant, SA2-13 was effective at inhibiting this IR enzyme and formed a trans-enamine inhibitory intermediate similar to the intermediate seen in the wt SHV-1 structure. Taken together, our data reveals that the C2 side chain linker length and composition profoundly affect the formation of the trans-enamine intermediate of penam sulfones. We also show that the design of SA2-13 derivatives offers promise against IR SHV β-lactamases that possess the K234R substitution.


    Organizational Affiliation

    Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, United States of America.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-lactamase SHV-1 A265Klebsiella pneumoniaeMutation(s): 1 
Gene Names: blashv1
EC: 3.5.2.6
Find proteins for P0AD64 (Klebsiella pneumoniae)
Explore P0AD64 
Go to UniProtKB:  P0AD64
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MA4
Query on MA4

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

Download Ideal Coordinates CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
0RJ
Query on 0RJ

Download Ideal Coordinates CCD File 
A
3-(formylamino)-L-alanine
C4 H8 N2 O3
VJGQHMAKHZCYRV-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.538α = 90
b = 55.259β = 90
c = 83.819γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description