Evidence map›Paper›PMID 27609419›Full record

ArticleScientific reports2016

Crystal structures of the UDP-diacylglucosamine pyrophosphohydrase LpxH from Pseudomonas aeruginosa.

Chiaki Okada, Hiroko Wakabayashi, Momoko Kobayashi, Akira Shinoda, Isao Tanaka, Min Yao

Abstract read
In one paragraph

Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.

0numbers the graph read from it
0cells of the map it votes in
17citing 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

17 citing papers in PubMed.

  1. Review
  2. Review
  3. Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Review
  9. Nucleotide Sugars in Chemistry and Biology.Molecules (Basel, Switzerland) · 2020
    Review
  10. Structural basis of the UDP-diacylglucosamine pyrophosphohydrolase LpxH inhibition by sulfonyl piperazine antibiotics.Proceedings of the National Academy of Sciences of the United States of America · 2020
    Article
  11. Article
  12. Activity and structure ofThe Journal of biological chemistry · 2019
    Article
  13. Article
  14. Article
  15. Article
  16. Review
  17. Structure, inhibition, and regulation of essential lipid A enzymes.Biochimica et biophysica acta. Molecular and cell biology of lipids · 2017
    Review
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.

Chiaki OkadaFaculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan.
Hiroko WakabayashiFaculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan.
Momoko KobayashiGraduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan.
Akira ShinodaGraduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan.
Isao TanakaFaculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan.
Min YaoFaculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Lipid A (also known as endotoxin) is the hydrophobic portion of lipopolysaccharides. It is an essential membrane component required for the viability of gram-negative bacteria. The enzymes involved in its biosynthesis are attractive targets for the development of novel antibiotics. LpxH catalyzes the fourth step of the lipid A biosynthesis pathway and cleaves the pyrophosphate bond of UDP-2,3-diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate (lipid X) and UMP. Here we present the structures of LpxH from Pseudomonas aeruginosa (PaLpxH). PaLpxH consists of two domains: a catalytic domain that is homologous to the metallophosphoesterases and a helical insertion domain. Lipid X was captured in the crevice between these two domains, with its phosphate group facing the dinuclear metal (Mn(2+)) center and two acyl chains buried in the hydrophobic cavity. The structures reveal that a large conformational change occurs at the lipid X binding site surface upon the binding/release of the product molecule. Based on these observations, we propose a novel model for lipid X embedding, which involves the scissor-like movement of helix α6, resulting in the release of lipid X into the lipid bilayer.

Indexed as

Bacterial ProteinsCatalytic DomainCrystallography, X-RayGlycolipidsHydrophobic and Hydrophilic InteractionsLipid AModels, MolecularMutationProtein BindingProtein ConformationPseudomonas aeruginosaPyrophosphatasesBacterial ProteinsGlycolipidsLipid Alipid XPyrophosphatasesUDP-2,3-diacylglucosamine pyrophosphatase

Identifiers

PMID27609419
PMCPMC5016852

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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.