3LEZ

Crystal structure of a halotolerant bacterial beta-lactamase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An antibiotic-resistance enzyme from a deep-sea bacterium

Toth, M.Smith, C.Frase, H.Mobashery, S.Vakulenko, S.

(2010) J.Am.Chem.Soc. 132: 816-823

  • DOI: 10.1021/ja908850p

  • PubMed Abstract: 
  • We describe herein a highly proficient class A beta-lactamase OIH-1 from the bacterium Oceanobacillus iheyensis, whose habitat is the sediment at a depth of 1050 m in the Pacific Ocean. The OIH-1 structure was solved by molecular replacement and refi ...

    We describe herein a highly proficient class A beta-lactamase OIH-1 from the bacterium Oceanobacillus iheyensis, whose habitat is the sediment at a depth of 1050 m in the Pacific Ocean. The OIH-1 structure was solved by molecular replacement and refined at 1.25 A resolution. OIH-1 has evolved to be an extremely halotolerant beta-lactamase capable of hydrolyzing its substrates in the presence of NaCl at saturating concentration. Not only is this the most highly halotolerant bacterial enzyme structure known to date, it is also the highest resolution halophilic protein structure yet determined. Evolution of OIH-1 in the salinity of the ocean has resulted in a molecular surface that is coated with acidic residues, a marked difference from beta-lactamases of terrestrial sources. OIH-1 is the first example of an antibiotic-resistance enzyme that has evolved in the depths of the ocean in isolation from clinical selection and gives us an extraordinary glimpse into protein evolution under extreme conditions. It represents evidence for the existence of a reservoir of antibiotic-resistance enzymes in nature among microbial populations from deep oceanic sources.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A
260Oceanobacillus iheyensis (strain DSM 14371 / CIP 107618 / JCM 11309 / KCTC 3954 / HTE831)Mutation(s): 0 
EC: 3.5.2.6
Find proteins for Q8EMP8 (Oceanobacillus iheyensis (strain DSM 14371 / CIP 107618 / JCM 11309 / KCTC 3954 / HTE831))
Go to UniProtKB:  Q8EMP8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

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Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.154 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 55.980α = 90.00
b = 55.980β = 90.00
c = 165.890γ = 120.00
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance