5EKB

R2-like ligand-binding oxidase with aerobically reconstituted Mn/Fe cofactor (reconstituted in solution)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.074 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Divergent assembly mechanisms of the manganese/iron cofactors in R2lox and R2c proteins.

Kutin, Y.Srinivas, V.Fritz, M.Kositzki, R.Shafaat, H.S.Birrell, J.Bill, E.Haumann, M.Lubitz, W.Hogbom, M.Griese, J.J.Cox, N.

(2016) J.Inorg.Biochem. 162: 164-177

  • DOI: 10.1016/j.jinorgbio.2016.04.019

  • PubMed Abstract: 
  • A manganese/iron cofactor which performs multi-electron oxidative chemistry is found in two classes of ferritin-like proteins, the small subunit (R2) of class Ic ribonucleotide reductase (R2c) and the R2-like ligand-binding oxidase (R2lox). It is unc ...

    A manganese/iron cofactor which performs multi-electron oxidative chemistry is found in two classes of ferritin-like proteins, the small subunit (R2) of class Ic ribonucleotide reductase (R2c) and the R2-like ligand-binding oxidase (R2lox). It is unclear how a heterodimeric Mn/Fe metallocofactor is assembled in these two related proteins as opposed to a homodimeric Fe/Fe cofactor, especially considering the structural similarity and proximity of the two metal-binding sites in both protein scaffolds and the similar first coordination sphere ligand preferences of MnII and FeII. Using EPR and Mössbauer spectroscopies as well as X-ray anomalous dispersion, we examined metal loading and cofactor activation of both proteins in vitro (in solution). We find divergent cofactor assembly mechanisms for the two systems. In both cases, excess MnII promotes heterobimetallic cofactor assembly. In the absence of FeII, R2c cooperatively binds MnII at both metal sites, whereas R2lox does not readily bind MnII at either site. Heterometallic cofactor assembly is favored at substoichiometric FeII concentrations in R2lox. FeII and MnII likely bind to the protein in a stepwise fashion, with FeII binding to site 2 initiating cofactor assembly. In R2c, however, heterometallic assembly is presumably achieved by the displacement of MnII by FeII at site 2. The divergent metal loading mechanisms are correlated with the putative in vivo functions of R2c and R2lox, and most likely with the intracellular MnII/FeII concentrations in the host organisms from which they were isolated.


    Organizational Affiliation

    Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonucleotide reductase small subunit
A
316Geobacillus kaustophilus (strain HTA426)Mutation(s): 0 
EC: 1.17.4.1
Find proteins for Q5KW80 (Geobacillus kaustophilus (strain HTA426))
Go to UniProtKB:  Q5KW80
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN3
Query on MN3

Download SDF File 
Download CCD File 
A
MANGANESE (III) ION
Mn
MMIPFLVOWGHZQD-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
PLM
Query on PLM

Download SDF File 
Download CCD File 
A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.074 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.190 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 56.041α = 90.00
b = 97.217β = 90.00
c = 128.279γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-05-11
    Type: Database references
  • Version 1.2: 2016-11-16
    Type: Database references
  • Version 1.3: 2018-03-07
    Type: Data collection
  • Version 1.4: 2019-02-20
    Type: Advisory, Data collection, Derived calculations