6EBP

Crystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit from Aerococcus urinae in Activated Form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Metal-free class Ie ribonucleotide reductase from pathogens initiates catalysis with a tyrosine-derived dihydroxyphenylalanine radical.

Blaesi, E.J.Palowitch, G.M.Hu, K.Kim, A.J.Rose, H.R.Alapati, R.Lougee, M.G.Kim, H.J.Taguchi, A.T.Tan, K.O.Laremore, T.N.Griffin, R.G.Krebs, C.Matthews, M.L.Silakov, A.Bollinger Jr., J.M.Allen, B.D.Boal, A.K.

(2018) Proc Natl Acad Sci U S A 115: 10022-10027

  • DOI: https://doi.org/10.1073/pnas.1811993115
  • Primary Citation of Related Structures:  
    6EBO, 6EBP, 6EBQ, 6EBZ

  • PubMed Abstract: 

    All cells obtain 2'-deoxyribonucleotides for DNA synthesis through the activity of a ribonucleotide reductase (RNR). The class I RNRs found in humans and pathogenic bacteria differ in ( i ) use of Fe(II), Mn(II), or both for activation of the dinuclear-metallocofactor subunit, β; ( ii ) reaction of the reduced dimetal center with dioxygen or superoxide for this activation; ( iii ) requirement (or lack thereof) for a flavoprotein activase, NrdI, to provide the superoxide from O 2 ; and ( iv ) use of either a stable tyrosyl radical or a high-valent dimetal cluster to initiate each turnover by oxidizing a cysteine residue in the α subunit to a radical (Cys•). The use of manganese by bacterial class I, subclass b-d RNRs, which contrasts with the exclusive use of iron by the eukaryotic Ia enzymes, appears to be a countermeasure of certain pathogens against iron deprivation imposed by their hosts. Here, we report a metal-free type of class I RNR (subclass e) from two human pathogens. The Cys• in its α subunit is generated by a stable, tyrosine-derived dihydroxyphenylalanine radical (DOPA•) in β. The three-electron oxidation producing DOPA• occurs in Escherichia coli only if the β is coexpressed with the NrdI activase encoded adjacently in the pathogen genome. The independence of this new RNR from transition metals, or the requirement for a single metal ion only transiently for activation, may afford the pathogens an even more potent countermeasure against transition metal-directed innate immunity.


  • Organizational Affiliation

    Department of Chemistry, The Pennsylvania State University, University Park, PA 16802.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase, beta subunit
A, B, C, D
355Aerococcus sp. Group 1Mutation(s): 0 
Gene Names: HMPREF9243_0731
EC: 1.17.4.1
UniProt
Find proteins for F2I8X9 (Aerococcus urinae (strain CCUG 59500 / ACS-120-V-Col10a))
Explore F2I8X9 
Go to UniProtKB:  F2I8X9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2I8X9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
L [auth C],
M [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
J [auth B]
K [auth C]
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth C],
N [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
DAH
Query on DAH
A, B, C, D
L-PEPTIDE LINKINGC9 H11 N O4PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.004α = 90
b = 109.417β = 90.06
c = 83.861γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM119707

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-17
    Changes: Data collection, Database references
  • Version 1.3: 2019-01-30
    Changes: Data collection, Structure summary
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2024-10-30
    Changes: Structure summary