Evidence map›Paper›PMID 23676677›Full record

ArticleNature2013

Crystal structure of the integral membrane diacylglycerol kinase.

Dianfan Li, Joseph A Lyons, Valerie E Pye, Lutz Vogeley, David Aragão, Colin P Kenyon, Syed T A Shah, Christine Doherty, Margaret Aherne, Martin Caffrey

Open access · greenAbstract read
In one paragraph

Article in Nature, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.

0numbers the graph read from it
0cells of the map it votes in
56citing papers in PubMed
7.3field-weighted citation impact, top 2% 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

56 citing papers in PubMed, 94 citations in OpenAlex.

  1. Article
  2. Article
  3. 7.10 MAG. A Novel Host Monoacylglyceride forCrystal growth & design · 2024
    Article
  4. Article
  5. Review
  6. Article
  7. Article
  8. Article
  9. Article
  10. Review
  11. Article
  12. Review
  13. Chemical tools for membrane protein structural biology.Current opinion in structural biology · 2019
    Review
  14. Article
  15. Article
  16. Article
  17. Article
  18. Diacylglycerol kinases: Relationship to other lipid kinases.Advances in biological regulation · 2019
    Review
  19. Membrane properties that shape the evolution of membrane enzymes.Current opinion in structural biology · 2018
    Review
  20. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors at 2 institutions in 3 countries.

Dianfan LiSchool of Biochemistry and Immunology & School of Medicine, Trinity College Dublin, Dublin 2, Ireland.
Joseph A Lyons
Valerie E Pye
Lutz Vogeley
David Aragão
Colin P Kenyon
Syed T A Shah
Christine Doherty
Margaret Aherne
Martin Caffrey
Trinity College Dublin · IECouncil for Scientific and Industrial Research · ZA

Funding

Y-FAMILY POLYMERASES AND CO-FACTORS IN TRANSLESION REPLICATIONP41RR015301 · NCRR · CORNELL UNIVERSITY ITHACA · PI EISENBERG, DAVID · 2001 to 2011
$28.2M
Yeast ExpressionP50GM073210 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI STROUD, ROBERT M · 2004 to 2013
$21.5M
Project 6 (Holton)U54GM094625 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI STROUD, ROBERT M · 2010 to 2014
$8.0M
Center for the Rational Design of Membrane Protein CrystallographyU54GM094599 · NIGMS · ARIZONA STATE UNIVERSITY-TEMPE CAMPUS · PI FROMME, PETRA · 2010 to 2014
$6.8M
Membrane Proteins. Crystallogenesis/X-ray Structure(RMI)R01GM075915 · NIGMS · UNIVERSITY OF LIMERICK · PI CAFFREY, MARTIN D. · 2005 to 2009
$984k
NCRR NIH HHS P41 RR015301NIGMS NIH HHS GM75915NIGMS NIH HHS P50 GM073210NIGMS NIH HHS P50GM073210NIGMS NIH HHS R01 GM075915NIGMS NIH HHS U54 GM094599NIGMS NIH HHS U54GM094599NIGMS NIH HHS U54 GM094625
6 · The paper itself

Abstract

Diacylglycerol kinase catalyses the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid for use in shuttling water-soluble components to membrane-derived oligosaccharide and lipopolysaccharide in the cell envelope of Gram-negative bacteria. For half a century, this 121-residue kinase has served as a model for investigating membrane protein enzymology, folding, assembly and stability. Here we present crystal structures for three functional forms of this unique and paradigmatic kinase, one of which is wild type. These reveal a homo-trimeric enzyme with three transmembrane helices and an amino-terminal amphiphilic helix per monomer. Bound lipid substrate and docked ATP identify the putative active site that is of the composite, shared site type. The crystal structures rationalize extensive biochemical and biophysical data on the enzyme. They are, however, at variance with a published solution NMR model in that domain swapping, a key feature of the solution form, is not observed in the crystal structures.

Indexed as

Adenosine TriphosphateBacterial ProteinsCatalytic DomainCell MembraneCrystallography, X-RayDiacylglycerol KinaseEnzyme ActivationEnzyme StabilityLipidsMagnesiumMembrane ProteinsModels, MolecularMutant ProteinsNuclear Magnetic Resonance, BiomolecularProtein ConformationZincAdenosine TriphosphateBacterial ProteinsDiacylglycerol KinaseLipidsMagnesiumMembrane ProteinsMutant ProteinsZinc

Identifiers

PMID23676677
PMCPMC3740270
OpenAlexW2069181755

What OpenQuestion holds

Textmetadata
LicenceTDM
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.