1ONG

SHV-1 beta-lactamase with a penem inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibition of Class A and Class C Beta-Lactamases by Penems: Crystallographic Structures of a Novel 1,4-Thiazepine Intermediate

Nukaga, M.Abe, T.Venkatesan, A.M.Mansour, T.S.Bonomo, R.A.Knox, J.R.

(2003) Biochemistry 42: 13152-13159

  • DOI: 10.1021/bi034986b
  • Primary Citation of Related Structures:  1ONH

  • PubMed Abstract: 
  • A new beta-lactamase inhibitor, a methylidene penem having a 5,6-dihydro-8H-imidazo[2,1-c][1,4]oxazine heterocyclic substituent at the C6 position with a Z configuration, irreversibly inhibits both class A and class C serine beta-lactamases with IC(5 ...

    A new beta-lactamase inhibitor, a methylidene penem having a 5,6-dihydro-8H-imidazo[2,1-c][1,4]oxazine heterocyclic substituent at the C6 position with a Z configuration, irreversibly inhibits both class A and class C serine beta-lactamases with IC(50) values of 0.4 and 9.0 nM for TEM-1 and SHV-1 (class A), respectively, and 4.8 nM in AmpC (class C) beta-lactamases. The compound also inhibits irreversibly the class C extended-spectrum GC1 beta-lactamase (IC(50) = 6.2 nM). High-resolution crystallographic structures of a reaction intermediate of (5R)-(6Z)-6-(5,6-dihydro-8H-imidazo[2,1-c][1,4]oxazin-2-ylmethylene)-7-oxo-4-thia-1-azabicyclo[3.2.0]hept-2-ene-3-carboxylic acid 1 with the SHV-1 beta-lactamase and with the GC1 beta-lactamase have been determined by X-ray diffraction to resolutions of 1.10 and 1.38 A, respectively. The two complexes were refined to crystallographic R-factors (R(free)) of 0.141 (0.186) and 0.138 (0.202), respectively. Cryoquenching of the reaction of 1 with each beta-lactamase crystal produced a common, covalently bound intermediate. After acylation of the serine, a nucleophilic attack by the departing thiolate on the C6' atom yielded a novel seven-membered 1,4-thiazepine ring having R stereochemistry at the new C7 moiety. The orientation of this ring in each complex differs by a 180 degrees rotation about the bond to the acylated serine. The acyl ester bond is stabilized to hydrolysis through resonance stabilization with the dihydrothiazepine ring and by low occupancy or disorder of hydrolytic water molecules. In the class A complex, the buried water molecule on the alpha-face of the ester bond appears to be loosely bound or absent. In the class C complex, a water molecule on the beta-face is disordered and poorly activated for hydrolysis. Here, the acyl intermediate is unable to assist its own hydrolysis, as is thought to occur with many class C substrates.


    Organizational Affiliation

    Department of Molecular and Cell Biology, The University of Connecticut, Storrs, Connecticut 06269-3125, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-LACTAMASE SHV-1
A
265Klebsiella pneumoniaeGene 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
WY4
Query on WY4

Download SDF File 
Download CCD File 
A
7-(5,6-DIHYDRO-8H-IMIDAZO[2,1-C][1,4]OXAZIN-2-YL)-6-FORMYL-2,7-DIHYDRO- [1,4]THIAZEPINE-3-CARBOXYLIC ACID
C13 H13 N3 O4 S
CTKODGPKPNVQNS-GFCCVEGCSA-N
 Ligand Interaction
MA4
Query on MA4

Download SDF File 
Download CCD File 
A
CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE
C24 H44 O11
WUCWJXGMSXTDAV-QKMCSOCLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
WY4IC50: 9 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.141 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.555α = 90.00
b = 55.183β = 90.00
c = 85.315γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance