Evidence map›Paper›PMID 25784552›Full record

ArticleThe Journal of biological chemistry2015

The class III cyclobutane pyrimidine dimer photolyase structure reveals a new antenna chromophore binding site and alternative photoreduction pathways.

Patrick Scheerer, Fan Zhang, Jacqueline Kalms, David von Stetten, Norbert Krauß, Inga Oberpichler, Tilman Lamparter

Abstract read
In one paragraph

Article in The Journal of biological chemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
23citing papers in PubMed, 1 pooled it
–field-weighted citation impact
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

23 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. Article
  3. A structural decryption of cryptochromes.Frontiers in chemistry · 2024
    Review
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  16. Article
  17. Photolyase: Dynamics and electron-transfer mechanisms of DNA repair.Archives of biochemistry and biophysics · 2017
    Review
  18. Insights into the red algae and eukaryotic evolution from the genome ofProceedings of the National Academy of Sciences of the United States of America · 2017
    Article
  19. Article
  20. Searching for novel photolyases in UVC-resistant Antarctic bacteria.Extremophiles : life under extreme conditions · 2017
    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

7 authors.

Patrick ScheererFrom the Charité, University Medicine Berlin, Institute of Medical Physics and Biophysics (CC2), AG Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany, patrick.scheerer@charite.de.
Fan Zhangthe Karlsruhe Institute of Technology (KIT), Botanical Institute, Kaiserstr. 2, D-76131 Karlsruhe, Germany.
Jacqueline KalmsFrom the Charité, University Medicine Berlin, Institute of Medical Physics and Biophysics (CC2), AG Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany.
David von Stettenthe Structural Biology Group, European Synchroton Radiation Facility, CS 40220, F-38043 Grenoble Cedex 9, France, and.
Norbert Kraußthe Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London E1 4NS, United Kingdom.
Inga Oberpichlerthe Karlsruhe Institute of Technology (KIT), Botanical Institute, Kaiserstr. 2, D-76131 Karlsruhe, Germany, oberpichler@gsl.uni-luebeck.de.
Tilman Lamparterthe Karlsruhe Institute of Technology (KIT), Botanical Institute, Kaiserstr. 2, D-76131 Karlsruhe, Germany, tilman.lamparter@kit.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Photolyases are proteins with an FAD chromophore that repair UV-induced pyrimidine dimers on the DNA in a light-dependent manner. The cyclobutane pyrimidine dimer class III photolyases are structurally unknown but closely related to plant cryptochromes, which serve as blue-light photoreceptors. Here we present the crystal structure of a class III photolyase termed photolyase-related protein A (PhrA) of Agrobacterium tumefaciens at 1.67-Å resolution. PhrA contains 5,10-methenyltetrahydrofolate (MTHF) as an antenna chromophore with a unique binding site and mode. Two Trp residues play pivotal roles for stabilizing MTHF by a double π-stacking sandwich. Plant cryptochrome I forms a pocket at the same site that could accommodate MTHF or a similar molecule. The PhrA structure and mutant studies showed that electrons flow during FAD photoreduction proceeds via two Trp triads. The structural studies on PhrA give a clearer picture on the evolutionary transition from photolyase to photoreceptor.

Indexed as

Ultraviolet RaysAgrobacterium tumefaciensBinding SitesCrystallography, X-RayCytochromesDeoxyribodipyrimidine Photo-LyaseDNA DamageEnzyme StabilityEvolution, MolecularFlavin-Adenine DinucleotideModels, MolecularNucleic Acid ConformationOxidation-ReductionProtein Structure, TertiaryPyrimidine DimersTetrahydrofolates5,10-methenyltetrahydrofolateCytochromesDeoxyribodipyrimidine Photo-LyaseFlavin-Adenine DinucleotidePyrimidine DimersTetrahydrofolatesCryptochromeCrystal StructureDNA RepairFlavin Adenine Dinucleotide (FAD)Molecular EvolutionMutagenesis in VitroPhotobiologyPhotoreceptorPhotoreductionSite-directed Mutagenesis

Identifiers

PMID25784552
PMCPMC4416854

What OpenQuestion holds

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Registered trials

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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.