4R3B

Crystal structure of SHV-1 b-lactamase in complex with 6b-(hydroxymethyl)penicillanic acid sulfone PSR-283A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 

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Literature

Detecting a Quasi-stable Imine Species on the Reaction Pathway of SHV-1 beta-Lactamase and 6 beta-(Hydroxymethyl)penicillanic Acid Sulfone.

Che, T.Rodkey, E.A.Bethel, C.R.Shanmugam, S.Ding, Z.Pusztai-Carey, M.Nottingham, M.Chai, W.Buynak, J.D.Bonomo, R.A.van den Akker, F.Carey, P.R.

(2015) Biochemistry 54: 734-743

  • DOI: 10.1021/bi501197t
  • Primary Citation of Related Structures:  
    4R3B

  • PubMed Abstract: 
  • For the class A β-lactamase SHV-1, the kinetic and mechanistic properties of the clinically used inhibitor sulbactam are compared with the sulbactam analog substituted in its 6β position by a CH2OH group (6β-(hydroxymethyl)penicillanic acid). The 6β substitution improves both in vitro and microbiological inhibitory properties of sulbactam ...

    For the class A β-lactamase SHV-1, the kinetic and mechanistic properties of the clinically used inhibitor sulbactam are compared with the sulbactam analog substituted in its 6β position by a CH2OH group (6β-(hydroxymethyl)penicillanic acid). The 6β substitution improves both in vitro and microbiological inhibitory properties of sulbactam. Base hydrolysis of both compounds was studied by Raman and NMR spectroscopies and showed that lactam ring opening is followed by fragmentation of the dioxothiazolidine ring leading to formation of the iminium ion within 3 min. The iminium ion slowly loses a proton and converts to cis-enamine (which is a β-aminoacrylate) in 1 h for sulbactam and in 4 h for 6β-(hydroxymethyl) sulbactam. Rapid mix-rapid freeze Raman spectroscopy was used to follow the reactions between the two sulfones and SHV-1. Within 23 ms, a 10-fold excess of sulbactam was entirely hydrolyzed to give a cis-enamine product. In contrast, the 6β-(hydroxymethyl) sulbactam formed longer-lived acyl-enzyme intermediates that are a mixture of imine and enamines. Single crystal Raman studies, soaking in and washing out unreacted substrates, revealed stable populations of imine and trans-enamine acyl enzymes. The corresponding X-ray crystallographic data are consonant with the Raman data and also reveal the role played by the 6β-hydroxymethyl group in retarding hydrolysis of the acyl enzymes. The 6β-hydroxymethyl group sterically hinders approach of the water molecule as well as restraining the side chain of E166 that facilitates hydrolysis.


    Organizational Affiliation

    Department of Biochemistry, ‡Department of Molecular Biology and Microbiology, §Department of Pharmacology, and ∥Department of Medicine, Case Western Reserve University , Cleveland, Ohio 44106, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-lactamase SHV-1A265Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blashv1
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MA4
Query on MA4

Download Ideal Coordinates CCD File 
B [auth A],
D [auth A]
CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE
C24 H44 O11
WUCWJXGMSXTDAV-QKMCSOCLSA-N
 Ligand Interaction
3GE
Query on 3GE

Download Ideal Coordinates CCD File 
C [auth A](2S)-3-[bis(oxidanylidene)-$l^{5}-sulfanyl]-2-[[2-(hydroxymethyl)-3-oxidanyl-propyl]amino]-3-methyl-butanoic acid
C9 H18 N O6 S
DNKMWLLNEKWQGX-ZETCQYMHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.238α = 90
b = 55.274β = 90
c = 84.465γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-02-11
    Changes: Database references