5GLC

Crystal structure of the class A beta-lactamase PenL-tTR11 containing 20 residues insertion in omega-loop


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.601 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

High adaptability of the omega loop underlies the substrate-spectrum-extension evolution of a class A beta-lactamase, PenL

Yi, H.Choi, J.M.Hwang, J.Prati, F.Cao, T.P.Lee, S.H.Kim, H.S.

(2016) Sci Rep 6: 36527-36527

  • DOI: 10.1038/srep36527
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The omega loop in β-lactamases plays a pivotal role in substrate recognition and catalysis, and some mutations in this loop affect the adaptability of the enzymes to new antibiotics. Various mutations, including substitutions, deletions, and intragen ...

    The omega loop in β-lactamases plays a pivotal role in substrate recognition and catalysis, and some mutations in this loop affect the adaptability of the enzymes to new antibiotics. Various mutations, including substitutions, deletions, and intragenic duplications resulting in tandem repeats (TRs), have been associated with β-lactamase substrate spectrum extension. TRs are unique among the mutations as they cause severe structural perturbations in the enzymes. We explored the process by which TRs are accommodated in order to test the adaptability of the omega loop. Structures of the mutant enzymes showed that the extra amino acid residues in the omega loop were freed outward from the enzyme, thereby maintaining the overall enzyme integrity. This structural adjustment was accompanied by disruptions of the internal α-helix and hydrogen bonds that originally maintained the conformation of the omega loop and the active site. Consequently, the mutant enzymes had a relaxed binding cavity, allowing for access of new substrates, which regrouped upon substrate binding in an induced-fit manner for subsequent hydrolytic reactions. Together, the data demonstrate that the design of the binding cavity, including the omega loop with its enormous adaptive capacity, is the foundation of the continuous evolution of β-lactamases against new drugs.


    Organizational Affiliation

    Department of Biomedical Sciences, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 136-705, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A
288Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264)Mutation(s): 0 
EC: 3.5.2.6
Find proteins for Q2T5A3 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264))
Go to UniProtKB:  Q2T5A3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.601 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 69.486α = 90.00
b = 97.242β = 90.00
c = 34.004γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research FoundationKorea, Republic Of2010-0005114
National Research FoundationKorea, Republic Of2013R1A1A2057465

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release