5NRT

Cys-Gly dipeptidase GliJ in complex with Ca2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Gliotoxin Biosynthesis: Structure, Mechanism, and Metal Promiscuity of Carboxypeptidase GliJ.

Marion, A.Groll, M.Scharf, D.H.Scherlach, K.Glaser, M.Sievers, H.Schuster, M.Hertweck, C.Brakhage, A.A.Antes, I.Huber, E.M.

(2017) ACS Chem. Biol. 12: 1874-1882

  • DOI: 10.1021/acschembio.6b00847
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The formation of glutathione (GSH) conjugates, best known from the detoxification of xenobiotics, is a widespread strategy to incorporate sulfur into biomolecules. The biosynthesis of gliotoxin, a virulence factor of the human pathogenic fungus Asper ...

    The formation of glutathione (GSH) conjugates, best known from the detoxification of xenobiotics, is a widespread strategy to incorporate sulfur into biomolecules. The biosynthesis of gliotoxin, a virulence factor of the human pathogenic fungus Aspergillus fumigatus, involves attachment of two GSH molecules and their sequential decomposition to yield two reactive thiol groups. The degradation of the GSH moieties requires the activity of the Cys-Gly carboxypeptidase GliJ, for which we describe the X-ray structure here. The enzyme forms a homodimer with each monomer comprising one active site. Two metal ions are present per proteolytic center, thus assigning GliJ to the diverse family of dinuclear metallohydrolases. Depending on availability, Zn2+, Fe2+, Fe3+, Mn2+, Cu2+, Co2+, or Ni2+ ions are accepted as cofactors. Despite this high metal promiscuity, a preference for zinc versus iron and manganese was noted. Mutagenesis experiments revealed details of metal coordination, and molecular modeling delivered insights into substrate recognition and processing by GliJ. The latter results suggest a reaction mechanism in which the two scissile peptide bonds of one gliotoxin precursor molecule are hydrolyzed sequentially and in a given order.


    Organizational Affiliation

    Center for Integrated Protein Science Munich at the Department of Biosciences, Technische Universit√§t M√ľnchen , Emil-Erlenmeyer-Forum 8, D-85354 Freising, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptidase gliJ
A
401Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)Mutation(s): 0 
Gene Names: gliJ
EC: 3.4.13.19
Find proteins for Q4WMJ8 (Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100))
Go to UniProtKB:  Q4WMJ8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.179 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 98.650α = 90.00
b = 98.650β = 90.00
c = 106.450γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-04-25 
  • Released Date: 2017-05-31 
  • Deposition Author(s): Groll, M., Huber, E.M.

Funding OrganizationLocationGrant Number
Hans-Fischer-GesellschaftGermany--
DFGGermanySFB749

Revision History 

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-08-02
    Type: Database references