6EBQ | pdb_00006ebq

Crystal Structure of the Flavoprotein NrdI from Aerococcus urinae in Oxidized Form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.269 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 36.58 kDa 
  • Atom Count: 2,208 
  • Modeled Residue Count: 261 
  • Deposited Residue Count: 320 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein NrdI
A, B
160Aerococcus urinaeMutation(s): 0 
Gene Names: nrdICYJ29_07405
UniProt
Find proteins for A0ACD6B8K1 (Aerococcus urinae (strain CCUG 59500 / ACS-120-V-Col10a))
Explore A0ACD6B8K1 
Go to UniProtKB:  A0ACD6B8K1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B8K1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.269 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.444α = 90
b = 50.057β = 112.57
c = 64.272γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description