4TM7

Crystal structure of 6-phosphogluconolactonase from Mycobacterium smegmatis N131D mutant soaked with CuSO4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Enzyme repurposing of a hydrolase as an emergent peroxidase upon metal binding.

Fujieda, N.Schatti, J.Stuttfeld, E.Ohkubo, K.Maier, T.Fukuzumi, S.Ward, T.R.

(2015) Chem Sci 6: 4060-4065

  • DOI: 10.1039/c5sc01065a
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • As an alternative to Darwinian evolution relying on catalytic promiscuity, a protein may acquire auxiliary function upon metal binding, thus providing it with a novel catalytic machinery. Here we show that addition of cupric ions to a 6-phosphoglucon ...

    As an alternative to Darwinian evolution relying on catalytic promiscuity, a protein may acquire auxiliary function upon metal binding, thus providing it with a novel catalytic machinery. Here we show that addition of cupric ions to a 6-phosphogluconolactonase 6-PGLac bearing a putative metal binding site leads to the emergence of peroxidase activity (kcat 7.8 × 10-2 s-1, KM 1.1 × 10-5 M). Both X-ray crystallographic and EPR data of the copper-loaded enzyme Cu·6-PGLac reveal a bis-histidine coordination site, located within a shallow binding pocket capable of accommodating the o-dianisidine substrate.


    Organizational Affiliation

    Department of Chemistry , University of Basel , Spitalstrasse 51 , CH-4056 Basel , Switzerland . Email: fujieda@mls.eng.osaka-u.ac.jp ; Email: thomas.ward@unibas.ch.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-phosphogluconolactonase
A
256Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 1 
Gene Names: pgl
EC: 3.1.1.31
Find proteins for A0QWX6 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0QWX6
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CU1
Query on CU1

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Download CCD File 
A
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.149 
  • Space Group: P 32 1 2
Unit Cell:
Length (Å)Angle (°)
a = 42.520α = 90.00
b = 42.520β = 90.00
c = 222.700γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Database references, Derived calculations, Other, Source and taxonomy