5BOH

Crystal Structure of OXA-58 with the Substrate-Binding Cleft in a Closed State


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.158 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal Structure of OXA-58 with the Substrate-Binding Cleft in a Closed State: Insights into the Mobility and Stability of the OXA-58 Structure

Saino, H.Sugiyabu, T.Ueno, G.Yamamoto, M.Ishii, Y.Miyano, M.

(2015) PLoS One 10: e0145869-e0145869

  • DOI: https://doi.org/10.1371/journal.pone.0145869
  • Primary Citation of Related Structures:  
    5BOH

  • PubMed Abstract: 

    OXA-58 is a class D β-lactamase from the multi-drug resistant Acinetobacter baumannii. We determined the crystal structure of OXA-58 in a novel crystal, and revealed the structure of the substrate-binding cleft in a closed state, distinct from a previously reported OXA-58 crystal structure with the binding cleft in an open state. In the closed state, the movement of three loops (α3-α4, β6-β7, and β8-α10) forms an arch-like architecture over the binding cleft through interaction between the Phe113 residues of α3-α4 and Met225 of β6-β7. This structure suggests the involvement of these flexible loops in OXA-58 substrate binding. In contrast to the mobile loops, the Ω-loop appeared static, including the conserved loop residues and their hydrogen bonds; the pivotal residue Trp169 within the Ω-loop, ζ-carbamic acid of the modified base catalyst residue Lys86, and nucleophilic residue Ser83. The stability of OXA-58 was enhanced concomitant with an increase in the hydrolytic activity catalyzed by NaHCO3-dependent ζ-carbamic acid formation, with an EC50 of 0.34 mM. The W169A mutant enzyme was significantly thermally unstable even in the presence of 100 mM NaHCO3, whereas the S83A mutant was stabilized with NaHCO3-dependent activation. The ζ-carbamic acid was shown to increase not only OXA-58 hydrolytic activity but also OXA-58 stability through the formation of a hydrogen bond network connected to the Ω-loop with Ser83 and Trp169. Thus, the static Ω-loop is important for OXA-58 stability, whereas the mobile loops of the substrate-binding cleft form the basis for accommodation of the various substituents of β-lactam backbone.


  • Organizational Affiliation

    Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Sagamihara-shi, Kanagawa, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase252Acinetobacter baumanniiMutation(s): 0 
Gene Names: blaOXA-58bla-oxa-58bla-oxa58
EC: 3.5.2.6
UniProt
Find proteins for Q2TR58 (Acinetobacter baumannii)
Explore Q2TR58 
Go to UniProtKB:  Q2TR58
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2TR58
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.158 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.29α = 90
b = 75.29β = 90
c = 120.682γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata processing
SCALAdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of SciencJapan15K21356
MEXT-Supported Program for the Strategic Research Foundation at Private UniversitiesJapanS1311005

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-01-27
    Changes: Data collection
  • Version 1.2: 2020-02-19
    Changes: Data collection, Derived calculations
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection