5I5M

Shewanella denitrificans nitrous oxide reductase, Ca2+-reconstituted form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Role of Calcium in Secondary Structure Stabilization during Maturation of Nitrous Oxide Reductase.

Schneider, L.K.Einsle, O.

(2016) Biochemistry 55: 1433-1440

  • DOI: 10.1021/acs.biochem.5b01278
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The copper enzyme nitrous oxide reductase catalyzes the two-electron reduction of nitrous oxide N₂O to dinitrogen N₂. Its maturation largely occurs in the periplasm and includes the insertion of at least one Ca²⁺ ion per monomer. Here we have investi ...

    The copper enzyme nitrous oxide reductase catalyzes the two-electron reduction of nitrous oxide N₂O to dinitrogen N₂. Its maturation largely occurs in the periplasm and includes the insertion of at least one Ca²⁺ ion per monomer. Here we have investigated the role of this structural cation in recombinantly produced apo-N₂OR from Shewanella denitrificans and have determined the three-dimensional structure of the protein by X-ray crystallography. In the absence of Ca²⁺, substantial parts of the enzyme surrounding the binding sites for the copper ions show structural disorder. Reconstitution of the binuclear CuA site was possible in vitro but required the presence of Ca²⁺ ions for a stable insertion of the center. In contrast, an excess of Ca²⁺ prevented copper insertion, and the structural analysis of the Ca²⁺apo form revealed that the cation is sufficient to structure the disordered regions of the protein even in the absence of Cu ions, indicating that the geometry of the two noncanonical copper centers is largely predetermined by the protein structure.


    Organizational Affiliation

    Institute for Biochemistry, Albert-Ludwigs-University Freiburg , 79104 Freiburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitrous-oxide reductase
A, B
638Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)Mutation(s): 0 
Gene Names: nosZ
EC: 1.7.2.4
Find proteins for Q12M27 (Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013))
Go to UniProtKB:  Q12M27
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BU3
Query on BU3

Download SDF File 
Download CCD File 
A, B
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.163 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 124.756α = 90.00
b = 56.978β = 105.58
c = 163.524γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilGermany310656
German Research FoundationGermanyRTG 1976

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-09
    Type: Database references
  • Version 1.2: 2016-03-23
    Type: Database references
  • Version 1.3: 2017-09-06
    Type: Author supporting evidence