Evidence map›Paper›PMID 23962108›Full record

ArticleBiochemistry2013

The periplasmic cavity of LacY mutant Cys154→Gly: how open is open?

Xiaoxu Jiang, Arnold J M Driessen, Ben L Feringa, H Ronald Kaback

Abstract read
In one paragraph

Article in Biochemistry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
0.9field-weighted citation impact, top 28% 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

5 citing papers in PubMed, 8 citations in OpenAlex.

  1. Oversized galactosides as a probe for conformational dynamics in LacY.Proceedings of the National Academy of Sciences of the United States of America · 2018
    Article
  2. Article
  3. A chemiosmotic mechanism of symport.Proceedings of the National Academy of Sciences of the United States of America · 2015
    Article
  4. Review
  5. Substrate-induced changes in the structural properties of LacY.Proceedings of the National Academy of Sciences of the United States of America · 2014
    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

4 authors at 1 institution in 1 country.

Xiaoxu JiangDepartment of Physiology and ‡Department of Microbiology, Immunology & Molecular Genertics, §Molecular Biology Institute, University of California Los Angeles , Los Angeles, California 90095, United States.
Arnold J M Driessen
Ben L Feringa
H Ronald Kaback
University of Groningen · NL

Funding

SPECIALIZED CENTER FOR THE PROTEIN STRUCTURE INITIATIVEU54GM074929 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI STAHLBERG, HENNING · 2005 to 2009
$16.6M
NEW APPROACHES TO MEMBRANE PROTEIN STRUCTURESR01DK051131 · NIDDK · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI KABACK, HOWARD RONALD · 1996 to 2014
$5.2M
Structural Basis for Mechanism of Secondary TransportersR01DK069463 · NIDDK · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI KABACK, HOWARD RONALD · 2005 to 2013
$3.7M
Structural Basis for Mechanism of Secondary TransportersR56DK069463 · NIDDK · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI KABACK, HOWARD RONALD · 2009 to 2009
$500k
Dynamics of the Lactose Permease of Escherichia ColiR56DK051131 · NIDDK · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI KABACK, HOWARD RONALD · 2015 to 2015
$154k
NIDDK NIH HHS DK069463NIDDK NIH HHS DK51131NIDDK NIH HHS R01 DK051131NIDDK NIH HHS R01 DK069463NIDDK NIH HHS R56 DK051131NIDDK NIH HHS R56 DK069463NIGMS NIH HHS GM074929NIGMS NIH HHS U54 GM074929
6 · The paper itself

Abstract

The lactose permease from Escherichia coli (LacY) is a galactoside/H(+) symporter that catalyzes the coupled stoichiometric transport of a sugar and an H(+) across the cytoplasmic membrane. X-ray crystal structures of WT LacY and the conformationally restricted mutant Cys154→Gly exhibit an inward-facing conformation with a tightly sealed periplasmic side and a deep central cleft or cavity open to the cytoplasm. Although the crystal structures may give the impression that LacY is a rigid molecule, multiple converging lines of evidence demonstrate that galactoside binding to WT LacY induces reciprocal opening and closing of periplasmic and cytoplasmic cavities, respectively. By this means, the sugar- and H(+)-binding sites in the middle of the molecule are exposed alternatively to either side of the membrane. In contrast to the crystal structure, biochemical/biophysical studies with mutant Cys154→Gly show that the periplasmic side is paralyzed in an open-outward conformation. In this study, a rigid, funnel-shaped, maleimide-containing molecule was used to probe the periplasmic cavity of a pseudo-WT and the Cys154→Gly mutant by site-directed alkylation. The findings provide strong support for previous observations and indicate further that the external opening of the periplasmic cleft in the mutant is patent to the extent of at least 8.5 Å in the absence of sugar or about half that of the WT cavity with bound galactoside.

Indexed as

Binding SitesCell MembraneCrystallography, X-RayCytoplasmEscherichia coli ProteinsGalactoseMaleimidesMembrane Transport ProteinsPeriplasmProtein ConformationTriphenylmethyl Compounds1-(4-tritylphenyl)pyrrole-2,5-dioneEscherichia coli ProteinsGalactoselactose permeaseMaleimidesMembrane Transport ProteinsTriphenylmethyl Compounds

Identifiers

PMID23962108
PMCPMC3951333
OpenAlexW2011501922

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.