4N83

X-ray crystal structure of Streptococcus sanguinis dimanganese(II)-NrdF

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS.

Makhlynets, O., Boal, A.K., Rhodes, D.V., Kitten, T., Rosenzweig, A.C., Stubbe, J.

(2014) J.Biol.Chem. 289: 6259-6272

  • DOI: 10.1074/jbc.M113.533554
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Streptococcus sanguinis is a causative agent of infective endocarditis. Deletion of SsaB, a manganese transporter, drastically reduces S. sanguinis virulence. Many pathogenic organisms require class Ib ribonucleotide reductase (RNR) to catalyze the c ...

    Streptococcus sanguinis is a causative agent of infective endocarditis. Deletion of SsaB, a manganese transporter, drastically reduces S. sanguinis virulence. Many pathogenic organisms require class Ib ribonucleotide reductase (RNR) to catalyze the conversion of nucleotides to deoxynucleotides under aerobic conditions, and recent studies demonstrate that this enzyme uses a dimanganese-tyrosyl radical (Mn(III)2-Y(•)) cofactor in vivo. The proteins required for S. sanguinis ribonucleotide reduction (NrdE and NrdF, α and β subunits of RNR; NrdH and TrxR, a glutaredoxin-like thioredoxin and a thioredoxin reductase; and NrdI, a flavodoxin essential for assembly of the RNR metallo-cofactor) have been identified and characterized. Apo-NrdF with Fe(II) and O2 can self-assemble a diferric-tyrosyl radical (Fe(III)2-Y(•)) cofactor (1.2 Y(•)/β2) and with the help of NrdI can assemble a Mn(III)2-Y(•) cofactor (0.9 Y(•)/β2). The activity of RNR with its endogenous reductants, NrdH and TrxR, is 5,000 and 1,500 units/mg for the Mn- and Fe-NrdFs (Fe-loaded NrdF), respectively. X-ray structures of S. sanguinis NrdIox and Mn(II)2-NrdF are reported and provide a possible rationale for the weak affinity (2.9 μM) between them. These streptococcal proteins form a structurally distinct subclass relative to other Ib proteins with unique features likely important in cluster assembly, including a long and negatively charged loop near the NrdI flavin and a bulky residue (Thr) at a constriction in the oxidant channel to the NrdI interface. These studies set the stage for identifying the active form of S. sanguinis class Ib RNR in an animal model for infective endocarditis and establishing whether the manganese requirement for pathogenesis is associated with RNR.

    Organizational Affiliation: 

    From the Departments of Chemistry and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonucleoside-diphosphate reductase subunit beta
A, B, C, D, E, F, G, H
319Streptococcus sanguinis (strain SK36)Mutation(s): 0 
Gene Names: nrdF
EC: 1.17.4.1
Find proteins for A3CLZ4 (Streptococcus sanguinis (strain SK36))
Go to UniProtKB:  A3CLZ4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 117.657α = 90.00
b = 80.224β = 105.91
c = 166.374γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
BALBESphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-08
    Type: Initial release
  • Version 1.1: 2014-02-26
    Type: Database references
  • Version 1.2: 2014-03-19
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description