Evidence map›Paper›PMID 39123319›Full record

ArticleFEBS open bio2024

Crystal structure of pectocin M1 reveals diverse conformations and interactions during its initial step via the ferredoxin uptake system.

Nawee Jantarit, Hideaki Tanaka, Yuxi Lin, Young-Ho Lee, Genji Kurisu

Abstract read
In one paragraph

Article in FEBS open bio, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

5 authors.

Nawee JantaritProtein Crystallography Laboratory, Institute for Protein Research, Osaka University, Suita, Japan.ORCID https://orcid.org/0000-0002-4179-3970
Hideaki TanakaProtein Crystallography Laboratory, Institute for Protein Research, Osaka University, Suita, Japan.
Yuxi LinBiopharmaceutical Research Center, Korea Basic Science Institute, Ochang, South Korea.
Young-Ho LeeBiopharmaceutical Research Center, Korea Basic Science Institute, Ochang, South Korea.
Genji KurisuProtein Crystallography Laboratory, Institute for Protein Research, Osaka University, Suita, Japan.ORCID https://orcid.org/0000-0002-5354-0807

Funding

JPS Grants-in-Aid for Scientific Research 23H04957JST-CREST JPMJCR20E1KBSI fund A412120KBSI fund A423100KBSI fund A439200National Research Foundation of Korea NRF-2022R1A2C1011793
6 · The paper itself

Abstract

Pectocin M1 (PM1), the bacteriocin from phytopathogenic Pectobacterium carotovorum which causes soft rot disease, has a unique ferredoxin domain that allows it to use FusA of the plant ferredoxin uptake system. To probe the structure-based mechanism of PM1 uptake, we determined the X-ray structure of full-length PM1, containing an N-terminal ferredoxin and C-terminal catalytic domain connected by helical linker, at 2.04 Å resolution. Based on published FusA structure and NMR data for PM1 ferredoxin domain titrated with FusA, we modeled docking of the ferredoxin domain with FusA. Combining the docking models with the X-ray structures of PM1 and FusA enables us to propose the mechanism by which PM1 undergoes dynamic domain rearrangement to translocate across the target cell outer membrane.

Indexed as

FerredoxinsBacterial ProteinsBacteriocinsCrystallography, X-RayModels, MolecularMolecular Docking SimulationPectobacterium carotovorumProtein ConformationBacterial ProteinsBacteriocinsFerredoxinsbacteriocinferredoxinlipid‐II‐degrading enzymePectobacteriumsiderophoreX‐ray crystallography

Identifiers

PMID39123319
PMCPMC11452297

What OpenQuestion holds

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LicenceCC BY
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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.