6SF5

Mn-containing form of the ribonucleotide reductase NrdB protein from Leeuwenhoekiella blandensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Class Id ribonucleotide reductase utilizes a Mn2(IV,III) cofactor and undergoes large conformational changes on metal loading.

Rozman Grinberg, I.Berglund, S.Hasan, M.Lundin, D.Ho, F.M.Magnuson, A.Logan, D.T.Sjoberg, B.M.Berggren, G.

(2019) J Biol Inorg Chem 24: 863-877

  • DOI: 10.1007/s00775-019-01697-8
  • Primary Citation of Related Structures:  
    6SF4, 6SF5

  • PubMed Abstract: 
  • Outside of the photosynthetic machinery, high-valent manganese cofactors are rare in biology. It was proposed that a recently discovered subclass of ribonucleotide reductase (RNR), class Id, is dependent on a Mn 2 (IV,III) cofactor for catalysis ...

    Outside of the photosynthetic machinery, high-valent manganese cofactors are rare in biology. It was proposed that a recently discovered subclass of ribonucleotide reductase (RNR), class Id, is dependent on a Mn 2 (IV,III) cofactor for catalysis. Class I RNRs consist of a substrate-binding component (NrdA) and a metal-containing radical-generating component (NrdB). Herein we utilize a combination of EPR spectroscopy and enzyme assays to underscore the enzymatic relevance of the Mn 2 (IV,III) cofactor in class Id NrdB from Facklamia ignava. Once formed, the Mn 2 (IV,III) cofactor confers enzyme activity that correlates well with cofactor quantity. Moreover, we present the X-ray structure of the apo- and aerobically Mn-loaded forms of the homologous class Id NrdB from Leeuwenhoekiella blandensis, revealing a dimanganese centre typical of the subclass, with a tyrosine residue maintained at distance from the metal centre and a lysine residue projected towards the metals. Structural comparison of the apo- and metal-loaded forms of the protein reveals a refolding of the loop containing the conserved lysine and an unusual shift in the orientation of helices within a monomer, leading to the opening of a channel towards the metal site. Such major conformational changes have not been observed in NrdB proteins before. Finally, in vitro reconstitution experiments reveal that the high-valent manganese cofactor is not formed spontaneously from oxygen, but can be generated from at least two different reduced oxygen species, i.e. H 2 O 2 and superoxide (O 2 ·- ). Considering the observed differences in the efficiency of these two activating reagents, we propose that the physiologically relevant mechanism involves superoxide.


    Organizational Affiliation

    Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala, Sweden. gustav.berggren@kemi.uu.se.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase, beta subunit 1A, B348Leeuwenhoekiella blandensisMutation(s): 0 
Gene Names: MED217_17135
EC: 1.17.4.1
UniProt
Find proteins for A3XHF9 (Leeuwenhoekiella blandensis (strain CECT 7118 / CCUG 51940 / MED217))
Explore A3XHF9 
Go to UniProtKB:  A3XHF9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3XHF9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.06α = 90
b = 80.602β = 90
c = 158.228γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2016-04855
Swedish Research CouncilSweden2016-01920
Wenner-Gren FoundationSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Derived calculations