5EKB

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


This is version 1.5 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
  • Primary Citation of Related Structures:  
    5EKB

  • 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 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 Mn II and Fe II ...

    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 Mn II and Fe II . 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 Mn II promotes heterobimetallic cofactor assembly. In the absence of Fe II , R2c cooperatively binds Mn II at both metal sites, whereas R2lox does not readily bind Mn II at either site. Heterometallic cofactor assembly is favored at substoichiometric Fe II concentrations in R2lox. Fe II and Mn II likely bind to the protein in a stepwise fashion, with Fe II binding to site 2 initiating cofactor assembly. In R2c, however, heterometallic assembly is presumably achieved by the displacement of Mn II by Fe II 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 Mn II /Fe II 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; Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia. Electronic address: nicholas.cox@cec.mpg.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonucleotide reductase small subunitA316Geobacillus kaustophilus HTA426Mutation(s): 0 
Gene Names: GK2771
EC: 1.17.4.1
UniProt
Find proteins for Q5KW80 (Geobacillus kaustophilus (strain HTA426))
Explore Q5KW80 
Go to UniProtKB:  Q5KW80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5KW80
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLM
Query on PLM

Download Ideal Coordinates CCD File 
D [auth A]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
C [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
MN3
Query on MN3

Download Ideal Coordinates CCD File 
B [auth A]MANGANESE (III) ION
Mn
MMIPFLVOWGHZQD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.041α = 90
b = 97.217β = 90
c = 128.279γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-05-11
    Changes: Database references
  • Version 1.2: 2016-11-16
    Changes: Database references
  • Version 1.3: 2018-03-07
    Changes: Data collection
  • Version 1.4: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.5: 2019-07-10
    Changes: Data collection