Evidence map›Paper›PMID 32523014›Full record

ArticleNature communications2020

An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism.

Mitchell G Thompson, Jacquelyn M Blake-Hedges, Jose Henrique Pereira, John A Hangasky, Michael S Belcher, William M Moore, Jesus F Barajas, Pablo Cruz-Morales, Lorenzo J Washington, Robert W Haushalter and 11 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Biocatalytic control of site-selectivity and chain length-selectivity in radical amino acid halogenases.Proceedings of the National Academy of Sciences of the United States of America · 2023
    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

21 authors.

Mitchell G Thompson *Joint BioEnergy Institute, Emeryville, CA, USA.ORCID http://orcid.org/0000-0002-1490-8074
Jacquelyn M Blake-Hedges *Joint BioEnergy Institute, Emeryville, CA, USA.
Jose Henrique Pereira *Joint BioEnergy Institute, Emeryville, CA, USA.
John A HangaskyDepartment of Chemistry, University of California-Berkeley, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-8386-3922
Michael S BelcherJoint BioEnergy Institute, Emeryville, CA, USA.ORCID http://orcid.org/0000-0003-2352-6817
William M MooreJoint BioEnergy Institute, Emeryville, CA, USA.
Jesus F BarajasJoint BioEnergy Institute, Emeryville, CA, USA.
Pablo Cruz-MoralesJoint BioEnergy Institute, Emeryville, CA, USA.
Lorenzo J WashingtonJoint BioEnergy Institute, Emeryville, CA, USA.
Robert W HaushalterJoint BioEnergy Institute, Emeryville, CA, USA.
Christopher B EibenJoint BioEnergy Institute, Emeryville, CA, USA.
Yuzhong LiuJoint BioEnergy Institute, Emeryville, CA, USA.
Will SkyrudDepartment of Chemistry, University of California-Berkeley, Berkeley, CA, USA.
Veronica T BenitesJoint BioEnergy Institute, Emeryville, CA, USA.
Tyler P BarnumDepartment of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA.
Edward E K BaidooJoint BioEnergy Institute, Emeryville, CA, USA.
Henrik V SchellerJoint BioEnergy Institute, Emeryville, CA, USA.ORCID http://orcid.org/0000-0002-6702-3560
Michael A MarlettaDepartment of Chemistry, University of California-Berkeley, Berkeley, CA, USA.ORCID http://orcid.org/0000-0001-8715-4253
Patrick M ShihJoint BioEnergy Institute, Emeryville, CA, USA.
Paul D AdamsJoint BioEnergy Institute, Emeryville, CA, USA.
Jay D KeaslingJoint BioEnergy Institute, Emeryville, CA, USA. jdkeasling@lbl.gov.ORCID http://orcid.org/0000-0003-4170-6088

Funding

X-ray Absorption Spectroscopy (XAS) pp.711-759P41GM103393 · NIGMS · STANFORD UNIVERSITY · PI HODGSON, KEITH O · 2012 to 2019
$30.6M
User Training and OutreachP30GM124169 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI PAUL David ADAMS, Gregory L Hura · 2017 to 2026
$28.6M
Howard Hughes Medical InstituteNIGMS NIH HHS P30 GM124169NIGMS NIH HHS P41 GM103393
6 · The paper itself

Abstract

Despite intensive study, plant lysine catabolism beyond the 2-oxoadipate (2OA) intermediate remains unvalidated. Recently we described a missing step in the D-lysine catabolism of Pseudomonas putida in which 2OA is converted to D-2-hydroxyglutarate (2HG) via hydroxyglutarate synthase (HglS), a DUF1338 family protein. Here we solve the structure of HglS to 1.1 Å resolution in substrate-free form and in complex with 2OA. We propose a successive decarboxylation and intramolecular hydroxylation mechanism forming 2HG in a Fe(II)- and O

Indexed as

ArabidopsisIronLysineOryzaOxygenasesPseudomonas putidaIronLysineOxygenases

Identifiers

PMID32523014
PMCPMC7286885

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.