4TM8 | pdb_00004tm8

Crystal structure of 6-phosphogluconolactonase from Mycobacterium smegmatis N131D mutant

• PDB DOI: https://doi.org/10.2210/pdb4TM8/pdb

• Classification: HYDROLASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-05-31 Released: 2015-06-03 
• Deposition Author(s): Fujieda, N., Stuttfeld, E., Maier, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.175 (Depositor) 
• R-Value Observed: 
  0.176 (Depositor) 

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

• PubMed: 29218172 
• DOI: https://doi.org/10.1039/c5sc01065a
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry , University of Basel , Spitalstrasse 51 , CH-4056 Basel , Switzerland . Email: [e-mail] ; Email: [e-mail].
Biozentrum , University of Basel , Klingelbergstr. 50/70 , CH-4056 Basel , Switzerland.
Department of Material and Life Science , Graduate School of Engineering , Osaka University , ALCA and SENTAN , Japan Science and Technology Agency (JST) , 2-1 Yamada-oka , Suita , Osaka 565-0871 , Japan.
Department of Bioinspired Science , Ewha Womans University , Seoul 120-750 , Korea.
Faculty of Science and Technology , Meijo University and ALCA and SENTAN , Japan Science and Technology Agency (JST) , Tempaku , Nagoya , Aichi 468-8502 , Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.04 kDa 
• Atom Count: 1,964 
• Modeled Residue Count: 245 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconolactonase	A	256	Mycolicibacterium smegmatis MC2 155	Mutation(s): 1  Gene Names: pgl, MSMEG_3099, MSMEI_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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.175 (Depositor) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.31	α = 90
b = 176.31	β = 90
c = 38.29	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-03 
Deposition Author(s): Fujieda, N., Stuttfeld, E., Maier, T.

Revision History  

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