5N76 | pdb_00005n76

Crystal structure of the apo-form of the CO dehydrogenase accessory protein CooT from Rhodospirillum rubrum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.282 (DCC) 
  • R-Value Work: 
    0.261 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5N76

This is version 1.3 of the entry. See complete history

Literature

The CO dehydrogenase accessory protein CooT is a novel nickel-binding protein.

Timm, J.Brochier-Armanet, C.Perard, J.Zambelli, B.Ollagnier-de-Choudens, S.Ciurli, S.Cavazza, C.

(2017) Metallomics 9: 575-583

  • DOI: https://doi.org/10.1039/c7mt00063d
  • Primary Citation Related Structures: 
    5N76

  • PubMed Abstract: 

    In Rhodospirillum rubrum, maturation of Carbon Monoxide Dehydrogenase (CODH) requires three accessory proteins, CooC, CooT and CooJ, dedicated to nickel insertion into the active site, which is constituted by a distorted [NiFe 3 S 4 ] cubane coordinated with a mononuclear Fe site. CooC is an ATPase proposed to provide the energy required for the maturation process, while CooJ is described as a metallochaperone with 16 histidines and 2 cysteines at the C-terminus, likely involved in metal binding and/or storage. Prior to the present study, no information was available on CooT at the molecular level. Here, the X-ray structure of RrCooT was obtained, which revealed that this protein is a homodimer featuring a fold that resembles an Sm-like domain, suggesting a role in RNA metabolism that was however not supported by experimental observations. Biochemical and biophysical evidence based on circular dichroism spectroscopy, light scattering, isothermal titration calorimetry and site-directed mutagenesis showed that RrCooT specifically binds a single Ni(ii) per dimer, with a dissociation constant of 9 nM, through the pair of Cys2, highly conserved residues, located at the dimer interface. Despite its role in the activation of RrCODH in vivo, CooT was thought to be a unique protein, found only in R. rubrum, with an unclear function. In this study, we extended the biological impact of CooT, establishing that this protein is a member of a novel Ni(ii)-binding protein family with 111 homologues, linked to anaerobic metabolism in bacteria and archaea, and in most cases to the presence of CODH.


  • Organizational Affiliation
    • Université Grenoble Alpes, Laboratoire de Chimie et Biologie des Métaux, BioCat, F-Grenoble, France.

Macromolecule Content 

  • Total Structure Weight: 42.63 kDa 
  • Atom Count: 3,047 
  • Modeled Residue Count: 371 
  • Deposited Residue Count: 396 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CooT66Rhodospirillum rubrumMutation(s): 0 
Gene Names: cooT
UniProt
Find proteins for P72320 (Rhodospirillum rubrum)
Explore P72320 
Go to UniProtKB:  P72320
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP72320
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.282 (DCC) 
  • R-Value Work:  0.261 (DCC) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.943α = 90
b = 108.943β = 90
c = 110.734γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fondation Simone Del DucaFranceCAJ-14-166

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-05-31
    Changes: Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Structure summary