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 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1039/c5sc01065a
  • Primary Citation of Related Structures:  
    4TM7, 4TM8

  • 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-phosphogluconolactonase 6-PGLac bearing a putative metal binding site leads to the emergence of peroxidase activity ( k cat 7.8 × 10 -2 s -1 , K M 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-phosphogluconolactonase256Mycolicibacterium smegmatis MC2 155Mutation(s): 1 
Gene Names: pglMSMEG_3099MSMEI_3021
EC: 3.1.1.31
UniProt
Find proteins for A0QWX6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QWX6 
Go to UniProtKB:  A0QWX6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QWX6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CU
Query on CU

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CU1
Query on CU1

Download Ideal Coordinates CCD File 
F [auth A]COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
V [auth A],
W [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.52α = 90
b = 42.52β = 90
c = 222.7γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations, Refinement description