Evidence map›Paper›PMID 29715329›Full record

ArticlePloS one2018

A new crystal form of Aspergillus oryzae catechol oxidase and evaluation of copper site structures in coupled binuclear copper enzymes.

Leena Penttinen, Chiara Rutanen, Markku Saloheimo, Kristiina Kruus, Juha Rouvinen, Nina Hakulinen

Open access · goldAbstract read
In one paragraph

Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.7field-weighted citation impact, top 35% 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

3 citing papers in PubMed, 11 citations in OpenAlex.

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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 2 institutions in 1 country.

Leena PenttinenDepartment of Chemistry, University of Eastern Finland Joensuu Campus, Joensuu, Finland.
Chiara RutanenDepartment of Chemistry, University of Eastern Finland Joensuu Campus, Joensuu, Finland.
Markku SaloheimoVTT Technical Research Center of Finland Ltd., Espoo, Finland.
Kristiina KruusVTT Technical Research Center of Finland Ltd., Espoo, Finland.
Juha RouvinenDepartment of Chemistry, University of Eastern Finland Joensuu Campus, Joensuu, Finland.
Nina HakulinenDepartment of Chemistry, University of Eastern Finland Joensuu Campus, Joensuu, Finland.ORCID 0000-0003-4471-7188
University of Eastern Finland · FIVTT Technical Research Centre of Finland · FI

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Coupled binuclear copper (CBC) enzymes have a conserved type 3 copper site that binds molecular oxygen to oxidize various mono- and diphenolic compounds. In this study, we found a new crystal form of catechol oxidase from Aspergillus oryzae (AoCO4) and solved two new structures from two different crystals at 1.8-Å and at 2.5-Å resolutions. These structures showed different copper site forms (met/deoxy and deoxy) and also differed from the copper site observed in the previously solved structure of AoCO4. We also analysed the electron density maps of all of the 56 CBC enzyme structures available in the protein data bank (PDB) and found that many of the published structures have vague copper sites. Some of the copper sites were then re-refined to find a better fit to the observed electron density. General problems in the refinement of metalloproteins and metal centres are discussed.

Indexed as

Aspergillus oryzaeBinding SitesCatechol OxidaseCopperCrystallography, X-RayOxidation-ReductionProtein ConformationCatechol OxidaseCopper

Identifiers

PMID29715329
PMCPMC5929527
OpenAlexW2801999662

What OpenQuestion holds

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LicenceCC BY
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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.