Evidence map›Paper›PMID 25516424›Full record

ArticleJournal of the American Chemical Society2015

Hydrogen bond network between amino acid radical intermediates on the proton-coupled electron transfer pathway of E. coli α2 ribonucleotide reductase.

Thomas U Nick, Wankyu Lee, Simone Kossmann, Frank Neese, JoAnne Stubbe, Marina Bennati

Open access · bronzeAbstract read
In one paragraph

Article in Journal of the American Chemical Society, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.

0numbers the graph read from it
0cells of the map it votes in
36citing papers in PubMed
3.6field-weighted citation impact, top 6% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

36 citing papers in PubMed, 67 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
  4. Review
  5. The critical role of a conserved lysine residue in periplasmic nitrate reductase catalyzed reactions.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2024
    Article
  6. Article
  7. Article
  8. Article
  9. Journal of the American Chemical Society · 2022
    Article
  10. Kinetic model for reversible radical transfer in ribonucleotide reductase.Proceedings of the National Academy of Sciences of the United States of America · 2022
    Article
  11. Article
  12. Article
  13. Radicals in Biology: Your Life Is in Their Hands.Journal of the American Chemical Society · 2021
    Article
  14. Article
  15. Review
  16. Statistical analysis of ENDOR spectra.Proceedings of the National Academy of Sciences of the United States of America · 2021
    Article
  17. Article
  18. Article
  19. Article
  20. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors at 3 institutions in 2 countries.

Thomas U NickMax Planck Institute for Biophysical Chemistry , 37077 Göttingen, Germany.
Wankyu Lee
Simone Kossmann
Frank Neese
JoAnne Stubbe
Marina Bennati
Massachusetts Institute of Technology · USMax Planck Institute for Biophysical Chemistry · DEMax Planck Institute for Chemical Energy Conversion · DE

Funding

Ribonucleotide Reductase: Structure and FunctionR01GM029595 · NIGMS · UNIVERSITY OF WISCONSIN MADISON · PI STUBBE, JOANNE · 1985 to 2016
$6.9M
MECHANISM OF DINUCLEAR FE-Y. FORMATION OF NDP REDUCTASER37GM029595 · NIGMS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI STUBBE, JOANNE · 1988 to 1997
–
NIGMS NIH HHS GM29595NIGMS NIH HHS R01 GM029595
6 · The paper itself

Abstract

Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides in all organisms. In all Class Ia RNRs, initiation of nucleotide diphosphate (NDP) reduction requires a reversible oxidation over 35 Å by a tyrosyl radical (Y122•, Escherichia coli) in subunit β of a cysteine (C439) in the active site of subunit α. This radical transfer (RT) occurs by a specific pathway involving redox active tyrosines (Y122 ⇆ Y356 in β to Y731 ⇆ Y730 ⇆ C439 in α); each oxidation necessitates loss of a proton coupled to loss of an electron (PCET). To study these steps, 3-aminotyrosine was site-specifically incorporated in place of Y356-β, Y731- and Y730-α, and each protein was incubated with the appropriate second subunit β(α), CDP and effector ATP to trap an amino tyrosyl radical (NH2Y•) in the active α2β2 complex. High-frequency (263 GHz) pulse electron paramagnetic resonance (EPR) of the NH2Y•s reported the gx values with unprecedented resolution and revealed strong electrostatic effects caused by the protein environment. (2)H electron-nuclear double resonance (ENDOR) spectroscopy accompanied by quantum chemical calculations provided spectroscopic evidence for hydrogen bond interactions at the radical sites, i.e., two exchangeable H bonds to NH2Y730•, one to NH2Y731• and none to NH2Y356•. Similar experiments with double mutants α-NH2Y730/C439A and α-NH2Y731/Y730F allowed assignment of the H bonding partner(s) to a pathway residue(s) providing direct evidence for colinear PCET within α. The implications of these observations for the PCET process within α and at the interface are discussed.

Indexed as

ProtonsAmino AcidsElectron TransportEscherichia coliFree RadicalsHydrogen BondingModels, MolecularMolecular ConformationRibonucleotide ReductasesAmino AcidsFree RadicalsProtonsRibonucleotide Reductases

Identifiers

PMID25516424
PMCPMC4304443
OpenAlexW2034859859

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.