Evidence map›Paper›PMID 26157133›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2015

Structure of LacY with an α-substituted galactoside: Connecting the binding site to the protonation site.

Hemant Kumar, Janet S Finer-Moore, H Ronald Kaback, Robert M Stroud

Abstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.

0numbers the graph read from it
0cells of the map it votes in
33citing 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

33 citing papers in PubMed.

  1. Structure and allostery in major facilitator superfamily symport mechanisms.Acta crystallographica. Section D, Structural biology · 2026
    Article
  2. Review
  3. Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Function Trumps Form in Two Sugar Symporters,International journal of molecular sciences · 2021
    Review
  9. Article
  10. The proton electrochemical gradient induces a kinetic asymmetry in the symport cycle of LacY.Proceedings of the National Academy of Sciences of the United States of America · 2020
    Article
  11. Article
  12. It takes two to tango: The dance of the permease.The Journal of general physiology · 2019
    Review
  13. Article
  14. Engineered occluded apo-intermediate of LacY.Proceedings of the National Academy of Sciences of the United States of America · 2018
    Article
  15. Article
  16. Crystal Structure of a ligand-bound LacY-Nanobody Complex.Proceedings of the National Academy of Sciences of the United States of America · 2018
    Article
  17. 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
  18. Article
  19. Proton movement and coupling in the POT family of peptide transporters.Proceedings of the National Academy of Sciences of the United States of America · 2017
    Article
  20. Ferrous iron efflux systems in bacteria.Metallomics : integrated biometal science · 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

4 authors.

Hemant KumarDepartment of Biochemistry and Biophysics, University of California, San Francisco, CA 94158;
Janet S Finer-MooreDepartment of Biochemistry and Biophysics, University of California, San Francisco, CA 94158;
H Ronald KabackDepartment of Physiology and Department of Microbiology, Immunology, and Molecular Genetics, and Molecular Biology Institute, University of California, Los Angeles, CA 90095 rkaback@mednet.ucla.edu stroud@msg.ucsf.edu.
Robert M StroudDepartment of Biochemistry and Biophysics, University of California, San Francisco, CA 94158; rkaback@mednet.ucla.edu stroud@msg.ucsf.edu.

Funding

STRUCTURE/FUNCTION OF PROTEINS AT MOLECULAR LEVELR01GM024485 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI STROUD, ROBERT M · 1985 to 2024
$7.5M
Molecular Basis for Transmembrane Conduction & SignalingR37GM024485 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI STROUD, ROBERT M · 2007 to 2016
$4.7M
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
NIDDK NIH HHS DK069463NIDDK NIH HHS R01 DK069463NIDDK NIH HHS R56 DK069463NIGMS NIH HHS R01 GM024485NIGMS NIH HHS R37 GM024485NIGMS NIH HHS R37GM024485
6 · The paper itself

Abstract

The X-ray crystal structure of a conformationally constrained mutant of the Escherichia coli lactose permease (the LacY double-Trp mutant Gly-46→Trp/Gly-262→Trp) with bound p-nitrophenyl-α-d-galactopyranoside (α-NPG), a high-affinity lactose analog, is described. With the exception of Glu-126 (helix IV), side chains Trp-151 (helix V), Glu-269 (helix VIII), Arg-144 (helix V), His-322 (helix X), and Asn-272 (helix VIII) interact directly with the galactopyranosyl ring of α-NPG to provide specificity, as indicated by biochemical studies and shown directly by X-ray crystallography. In contrast, Phe-20, Met-23, and Phe-27 (helix I) are within van der Waals distance of the benzyl moiety of the analog and thereby increase binding affinity nonspecifically. Thus, the specificity of LacY for sugar is determined solely by side-chain interactions with the galactopyranosyl ring, whereas affinity is increased by nonspecific hydrophobic interactions with the anomeric substituent.

Indexed as

ProtonsBinding SitesCrystallography, X-RayEscherichia coliEscherichia coli ProteinsLigandsModels, MolecularMonosaccharide Transport ProteinsNitrophenylgalactosidesProtein Structure, SecondaryStatic ElectricitySubstrate SpecificitySymporters4-nitrophenylgalactosideEscherichia coli ProteinsLacY protein, E coliLigandsMonosaccharide Transport ProteinsNitrophenylgalactosidesProtonsSymportersconformational changemajor facilitator superfamilymembrane proteintransportX-ray structure

Identifiers

PMID26157133
PMCPMC4517220

What OpenQuestion holds

Textmetadata
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.