6H3D

Staphylopine dehydrogenase in complex with xNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

Starting Model: experimental
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This is version 1.1 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
DUF2338 domain-containing protein441Staphylococcus aureusMutation(s): 0 
Gene Names: RK60_12795RK98_07680RL06_05590SAMEA3448991_00758
EC: 1.5.1.52
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.09α = 90
b = 48.75β = 90
c = 59.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description