6GMZ

Staphylopine dehydrogenase in complex with Histidine tag and citrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Control by Metals of Staphylopine Dehydrogenase Activity during Metallophore Biosynthesis.

Hajjar, C.Fanelli, R.Laffont, C.Brutesco, C.Cullia, G.Tribout, M.Nurizzo, D.Borezee-Durant, E.Voulhoux, R.Pignol, D.Lavergne, J.Cavelier, F.Arnoux, P.

(2019) J Am Chem Soc 141: 5555-5562

  • DOI: https://doi.org/10.1021/jacs.9b01676
  • Primary Citation of Related Structures:  
    6GMZ, 6H31, 6H3D, 6H3F

  • PubMed Abstract: 

    Enzymatic regulations are central processes for the adaptation to changing environments. In the particular case of metallophore-dependent metal uptake, there is a need to quickly adjust the production of these metallophores to the metal level outside the cell, to avoid metal shortage or overload, as well as waste of metallophores. In Staphylococcus aureus, CntM catalyzes the last biosynthetic step in the production of staphylopine, a broad-spectrum metallophore, through the reductive condensation of a pathway intermediate (xNA) with pyruvate. Here, we describe the chemical synthesis of this intermediate, which was instrumental in the structural and functional characterization of CntM and confirmed its opine synthase properties. The three-dimensional structure of CntM was obtained in an "open" form, in the apo state or as a complex with substrate or product. The xNA substrate appears mainly stabilized by its imidazole ring through a π-π interaction with the side chain of Tyr240. Intriguingly, we found that metals exerted various and sometime antagonistic effects on the reaction catalyzed by CntM: zinc and copper are moderate activators at low concentration and then total inhibitors at higher concentration, whereas manganese is only an activator and cobalt and nickel are only inhibitors. We propose a model in which the relative affinity of a metal toward xNA and an inhibitory binding site on the enzyme controls activation, inhibition, or both as a function of metal concentration. This metal-dependent regulation of a metallophore-producing enzyme might also take place in vivo, which could contribute to the adjustment of metallophore production to the internal metal level.


  • Organizational Affiliation

    Aix Marseille Université , CEA, CNRS, BIAM, F-13108 Saint Paul-Lez-Durance , France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Staphylopine dehydrogenase465Staphylococcus aureusMutation(s): 0 
Gene Names: APW47_05390
UniProt
Find proteins for A0A0H3JT80 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore A0A0H3JT80 
Go to UniProtKB:  A0A0H3JT80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3JT80
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-HIS-HIS-ALA4Staphylococcus aureusMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.44α = 90
b = 48.79β = 90
c = 60.16γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
CRANKphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-14-CE09-0007-02

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release