7OG7

Crystal structure of the copper chaperone NosL from Shewanella denitrificans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Copper Chaperone NosL Forms a Heterometal Site for Cu Delivery to Nitrous Oxide Reductase.

Prasser, B.Schoner, L.Zhang, L.Einsle, O.

(2021) Angew Chem Int Ed Engl 60: 18810-18814

  • DOI: https://doi.org/10.1002/anie.202106348
  • Primary Citation of Related Structures:  
    7OG7

  • PubMed Abstract: 

    The final step of denitrification is the reduction of nitrous oxide (N 2 O) to N 2 , mediated by Cu-dependent nitrous oxide reductase (N 2 OR). Its metal centers, Cu A and Cu Z , are assembled through sequential provision of twelve Cu I ions by a metallochaperone that forms part of a nos gene cluster encoding the enzyme and its accessory factors. The chaperone is the nosL gene product, an 18 kDa lipoprotein predicted to reside in the outer membrane of Gram-negative bacteria. In order to better understand the assembly of N 2 OR, we have produced NosL from Shewanella denitrificans and determined the structure of the metal-loaded chaperone by X-ray crystallography. The protein assembled a heterodinuclear metal site consisting of Zn II and Cu I , as evidenced by anomalous X-ray scattering. While only Cu I is delivered to the enzyme, the stabilizing presence of Zn II is essential for the functionality and structural integrity of the chaperone.


  • Organizational Affiliation

    Institut für Biochemie, Fakultät für Chemie und Pharmazie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NosL182Shewanella denitrificans OS217Mutation(s): 0 
Gene Names: Sden_2215
UniProt
Find proteins for Q12M31 (Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013))
Explore Q12M31 
Go to UniProtKB:  Q12M31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12M31
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: F 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.066α = 90
b = 179.066β = 90
c = 179.066γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
AutoSolphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)Germany310656
German Research Foundation (DFG)Germany235777276

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2021-08-18
    Changes: Database references