Evidence map›Paper›PMID 25102080›Full record

ArticleJournal of molecular biology2014

Identification of a unique Fe-S cluster binding site in a glycyl-radical type microcompartment shell protein.

Michael C Thompson, Nicole M Wheatley, Julien Jorda, Michael R Sawaya, Soheil D Gidaniyan, Hoda Ahmed, Zhongyu Yang, Krystal N McCarty, Julian P Whitelegge, Todd O Yeates

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of molecular biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing papers in PubMed
0.7field-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

12 citing papers in PubMed, 19 citations in OpenAlex.

  1. Review
  2. Article
  3. Review
  4. Article
  5. Review
  6. Article
  7. Review
  8. Article
  9. Bacterial microcompartments.Nature reviews. Microbiology · 2018
    Review
  10. Article
  11. Article
  12. 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

10 authors at 2 institutions in 1 country.

Michael C ThompsonDepartment of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.
Nicole M WheatleyMolecular Biology Interdepartmental Ph.D. Program, University of California, Los Angeles, CA 90095, USA.
Julien JordaUniversity of California, Los Angeles-Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA.
Michael R SawayaUniversity of California, Los Angeles-Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA.
Soheil D GidaniyanDepartment of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.
Hoda AhmedDepartment of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.
Zhongyu YangJules Stein Eye Institute, University of California, Los Angeles, CA 90095, USA.
Krystal N McCartyDepartment of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.
Julian P WhiteleggePasarow Mass Spectrometry Laboratory, Neuropsychiatric Institute-Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA 90095, USA.
Todd O YeatesDepartment of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; University of California, Los Angeles-Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA. Electronic address: yeates@mbi.ucla.edu.
University of California, Los Angeles · USHouse Clinic · US

Funding

Transgenic & Knock-out MouseP30DK063491 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PETER J TONTONOZ · 2003 to 2026
$40.4M
Y-FAMILY POLYMERASES AND CO-FACTORS IN TRANSLESION REPLICATIONP41RR015301 · NCRR · CORNELL UNIVERSITY ITHACA · PI EISENBERG, DAVID · 2001 to 2011
$28.2M
UCLA NIGMS T32 Program AssessmentT32GM007185 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI TORRES, JORGE · 1985 to 2020
$21.7M
Testing Hypotheses by Site Directed Mutagenesis of SOD1P01NS049134 · NINDS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI BORCHELT, DAVID R · 2005 to 2014
$10.9M
Dissecting the structure, function, and mechanisms of diverse protein-based metabolic organelles in bacteriaR01AI081146 · NIAID · IOWA STATE UNIVERSITY · PI BOBIK, THOMAS AQUINAS, YEATES, TODD O · 2009 to 2022
$6.5M
NCRR NIH HHS P41 RR015301NCRR NIH HHS RR-15301NIAID NIH HHS R01 AI081146NIAID NIH HHS R01AI081146NIDDK NIH HHS P30 DK063491NIGMS NIH HHS GM007185NIGMS NIH HHS T32 GM007185NINDS NIH HHS P01 NS049134
6 · The paper itself

Abstract

Recently, progress has been made toward understanding the functional diversity of bacterial microcompartment (MCP) systems, which serve as protein-based metabolic organelles in diverse microbes. New types of MCPs have been identified, including the glycyl-radical propanediol (Grp) MCP. Within these elaborate protein complexes, BMC-domain shell proteins [bacterial microcompartment (in reference to the shell protein domain)] assemble to form a polyhedral barrier that encapsulates the enzymatic contents of the MCP. Interestingly, the Grp MCP contains a number of shell proteins with unusual sequence features. GrpU is one such shell protein whose amino acid sequence is particularly divergent from other members of the BMC-domain superfamily of proteins that effectively defines all MCPs. Expression, purification, and subsequent characterization of the protein showed, unexpectedly, that it binds an iron-sulfur cluster. We determined X-ray crystal structures of two GrpU orthologs, providing the first structural insight into the homohexameric BMC-domain shell proteins of the Grp system. The X-ray structures of GrpU, both obtained in the apo form, combined with spectroscopic analyses and computational modeling, show that the metal cluster resides in the central pore of the BMC shell protein at a position of broken 6-fold symmetry. The result is a structurally polymorphic iron-sulfur cluster binding site that appears to be unique among metalloproteins studied to date.

Indexed as

Amino Acid SequenceBacterial ProteinsBinding SitesClostridiumCrystallography, X-RayIron-Sulfur ProteinsModels, MolecularPectobacteriumPropylene GlycolsProtein Structure, TertiaryBacterial ProteinsIron-Sulfur ProteinsPropylene GlycolsBMC-domainconformational polymorphismglycyl-radical propanediol (Grp)metalloproteinsymmetry-breaking

Identifiers

PMID25102080
PMCPMC4175982
OpenAlexW2087812442

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.