6H3F

Staphylopine dehydrogenase in complex with staphylopine and NADP+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
Staphylopine dehydrogenase441Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: SA2256
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
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
B [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
8UX
Query on 8UX

Download Ideal Coordinates CCD File 
C [auth A](2~{S})-4-[[(2~{R})-3-(1~{H}-imidazol-4-yl)-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-[[(2~{S})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]butanoic acid
C13 H20 N4 O6
WLNNYKMTYVPSDL-UJNFCWOMSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
E [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 187.18α = 90
b = 49.14β = 90
c = 58.71γ = 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