Evidence map›Paper›PMID 30097100›Full record

ArticleMethods in enzymology2018

Methods for Expression, Purification, and Characterization of PqqE, a Radical SAM Enzyme in the PQQ Biosynthetic Pathway.

Wen Zhu, Ana M Martins, Judith P Klinman

Abstract read
In one paragraph

Article in Methods in enzymology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing 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

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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

9 citing papers in PubMed.

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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

3 authors.

Wen ZhuCalifornia Institute for Quantitative Biosciences, University of California, Berkeley, CA, United States; Department of Chemistry, University of California, Berkeley, CA, United States.
Ana M MartinsCalifornia Institute for Quantitative Biosciences, University of California, Berkeley, CA, United States.
Judith P KlinmanCalifornia Institute for Quantitative Biosciences, University of California, Berkeley, CA, United States; Department of Chemistry, University of California, Berkeley, CA, United States; Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States. Electronic address: klinman@berkeley.edu.

Funding

Looking in New Directions for Origins and Cryptic Mechanisms of Enzyme CatalysisR35GM118117 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI KLINMAN, JUDITH P · 2016 to 2025
$7.5M
NIGMS NIH HHS R35 GM118117
6 · The paper itself

Abstract

PqqE is the first enzyme in the biosynthetic pathway of the redox cofactor pyrroloquinoline quinone (PQQ), catalyzing the formation of a carbon-carbon bond in the precursor peptide PqqA. PqqE is a radical S-adenosyl-l-methionine (SAM) (RS) enzyme, a family of enzymes that use the reductive cleavage of a [4Fe-4S] cluster-bound SAM molecule to generate a 5'-deoxyadenosyl radical. This radical is then used to initiate an array of reactions that otherwise would be unlikely to occur. PqqE is a founding member of a subset family of RS enzymes that, additionally to the SAM [4Fe-4S] cluster, have a SPASM domain containing additional, auxiliary Fe-S clusters. Most radical SAM enzymes are highly sensitive to oxygen, which destroys their Fe-S clusters. This can pose several limitations when working with these enzymes, since most of the work has to be done under anaerobic conditions. Here, we summarize the methods developed in our lab for the expression and purification of PqqE. We also highlight the several methods we have used for the characterization of the enzyme.

Indexed as

AnaerobiosisBacterial ProteinsBiosynthetic PathwaysEndopeptidasesEnzyme AssaysPQQ CofactorRecombinant ProteinsS-AdenosylmethionineSequence AlignmentBacterial ProteinsEndopeptidasesPQQ CofactorPqqE protein, Methylobacterium extorquensRecombinant ProteinsS-AdenosylmethionineEPRFe–S clustersMössbauer spectroscopyPQQ biosynthesisPqqEProtein interactionRadical SAM

Identifiers

PMID30097100
PMCPMC6287933

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.