6SKP

OXA-10_IPM. Structural insight to the enhanced carbapenem efficiency of OXA-655 compared to OXA-10.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the enhanced carbapenemase efficiency of OXA-655 compared to OXA-10.

Leiros, H.S.Thomassen, A.M.Samuelsen, O.Flach, C.F.Kotsakis, S.D.Larsson, D.G.J.

(2020) FEBS Open Bio 10: 1821-1832

  • DOI: 10.1002/2211-5463.12935
  • Primary Citation of Related Structures:  
    6SKP, 6SKQ, 6SKR

  • PubMed Abstract: 
  • Carbapenemases are the main cause of carbapenem resistance in Gram-negative bacteria. How β-lactamases with weak carbapenemase activity, such as the OXA-10-type class D β-lactamases, contribute to anti-bacterial drug resistance is unclear. OXA-655 is a T26M and V117L OXA-10 variant, recently identified from hospital wastewater ...

    Carbapenemases are the main cause of carbapenem resistance in Gram-negative bacteria. How β-lactamases with weak carbapenemase activity, such as the OXA-10-type class D β-lactamases, contribute to anti-bacterial drug resistance is unclear. OXA-655 is a T26M and V117L OXA-10 variant, recently identified from hospital wastewater. Despite exhibiting stronger carbapenemase activity towards ertapenem (ETP) and meropenem (MEM) in Escherichia coli, OXA-655 exhibits reduced activity towards oxyimino-substituted β-lactams like ceftazidime. Here, we have solved crystal structures of OXA-10 in complex with imipenem (IPM) and ETP, and OXA-655 in complex with MEM in order to unravel the structure-function relationship and the impact of residue 117 in enzyme catalysis. The new crystal structures show that L117 is situated at a critical position with enhanced Van der Waals interactions to L155 in the omega loop. This restricts the movements of L155 and could explain the reduced ability for OXA-655 to bind a bulky oxyimino group. The V117L replacement in OXA-655 makes the active site S67 and the carboxylated K70 more water exposed. This could affect the supply of new deacylation water molecules required for hydrolysis and possibly the carboxylation rate of K70. But most importantly, L117 leaves more space for binding of the hydroxyethyl group in carbapenems. In summary, the crystal structures highlight the importance of residue 117 in OXA-10 variants for carbapenemase activity. This study also illustrates the impact of a single amino acid substitution on the substrate profile of OXA-10 and the evolutionary potential of new OXA-10 variants.


    Organizational Affiliation

    Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-lactamaseA, B266Escherichia coliMutation(s): 0 
Gene Names: 
EC: 3.5.2.6
UniProt
Find proteins for Q7BNC2 (Escherichia coli)
Explore Q7BNC2 
Go to UniProtKB:  Q7BNC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7BNC2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IM2 (Subject of Investigation/LOI)
Query on IM2

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
(5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid
C12 H19 N3 O4 S
UACUABDJLSUFFC-IWSPIJDZSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
F [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, B L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.933α = 90
b = 124.794β = 90
c = 48.48γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2019-08-16 
  • Released Date: 2019-09-18 
  • Deposition Author(s): Leiros, H.-K.S.

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2020-07-29
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.2: 2020-09-09
    Changes: Database references