Evidence map›Paper›PMID 26240141›Full record

ArticleThe Journal of biological chemistry2015

Structural Characterization of CalS8, a TDP-α-D-Glucose Dehydrogenase Involved in Calicheamicin Aminodideoxypentose Biosynthesis.

Shanteri Singh, Karolina Michalska, Lance Bigelow, Michael Endres, Madan K Kharel, Gyorgy Babnigg, Ragothaman M Yennamalli, Craig A Bingman, Andrzej Joachimiak, Jon S Thorson and 1 more

Open access · hybridAbstract read
In one paragraph

Article in The Journal of biological chemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.1field-weighted citation impact, top 53% 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

2 citing papers in PubMed, 6 citations in OpenAlex.

  1. Article
  2. 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

11 authors at 5 institutions in 1 country.

Shanteri SinghFrom the Center for Pharmaceutical Research and Innovation, University of Kentucky College of Pharmacy, Lexington, Kentucky 40536-0596.
Karolina Michalskathe Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439.
Lance Bigelowthe Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439.
Michael Endresthe Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439.
Madan K Kharelthe School of Pharmacy, University of Maryland Eastern Shore, Princess Anne, Maryland 21853.
Gyorgy Babniggthe Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439.
Ragothaman M Yennamallithe Department of BioSciences, Department of Chemistry, Rice University, Houston, Texas 77005.
Craig A Bingmanthe Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, and.
Andrzej Joachimiakthe Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439.
Jon S ThorsonFrom the Center for Pharmaceutical Research and Innovation, University of Kentucky College of Pharmacy, Lexington, Kentucky 40536-0596, jsthorson@uky.edu.
George N Phillipsthe Department of BioSciences, Department of Chemistry, Rice University, Houston, Texas 77005 the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, and georgep@rice.edu.
Joint Center for Structural Genomics · USUniversity of Kentucky · USArgonne National Laboratory · USUniversity of Maryland Eastern Shore · USUniversity of Wisconsin–Madison · US

Funding

Midwest Center for Structural GenomicsU54GM094585 · NIGMS · UNIVERSITY OF CHICAGO · PI MINOR, WLADEK · 2010 to 2014
$33.7M
Kentucky Center for Clinical and Translational ScienceUL1TR000117 · NCATS · UNIVERSITY OF KENTUCKY · PI KERN, PHILIP A · 2012 to 2015
$13.3M
In Vitro Glycorandomization of Natural ProductsR37AI052218 · NIAID · UNIVERSITY OF KENTUCKY · PI THORSON, JON SCOTT · 2012 to 2021
$4.0M
STUDIES ON CALICHEAMICIN BIOSYNTHESIS AND SELF RESISTANCER01CA084374 · NCI · UNIVERSITY OF WISCONSIN-MADISON · PI THORSON, JON SCOTT · 2000 to 2013
$3.6M
Enzyme Discovery for Natural Product BiosynthesisU01GM098248 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI PHILLIPS, GEORGE NEAL · 2011 to 2015
$2.8M
NCATS NIH HHS UL1 TR000117NCATS NIH HHS UL1TR000117NCI NIH HHS R01 CA084374NCI NIH HHS R01 CA84374NIAID NIH HHS R37 AI052218NIGMS NIH HHS GM094585NIGMS NIH HHS U01 GM098248NIGMS NIH HHS U01GM098248NIGMS NIH HHS U54 GM094585
6 · The paper itself

Abstract

Classical UDP-glucose 6-dehydrogenases (UGDHs; EC 1.1.1.22) catalyze the conversion of UDP-α-d-glucose (UDP-Glc) to the key metabolic precursor UDP-α-d-glucuronic acid (UDP-GlcA) and display specificity for UDP-Glc. The fundamental biochemical and structural study of the UGDH homolog CalS8 encoded by the calicheamicin biosynthetic gene is reported and represents one of the first studies of a UGDH homolog involved in secondary metabolism. The corresponding biochemical characterization of CalS8 reveals CalS8 as one of the first characterized base-permissive UGDH homologs with a >15-fold preference for TDP-Glc over UDP-Glc. The corresponding structure elucidations of apo-CalS8 and the CalS8·substrate·cofactor ternary complex (at 2.47 and 1.95 Å resolution, respectively) highlight a notably high degree of conservation between CalS8 and classical UGDHs where structural divergence within the intersubunit loop structure likely contributes to the CalS8 base permissivity. As such, this study begins to provide a putative blueprint for base specificity among sugar nucleotide-dependent dehydrogenases and, in conjunction with prior studies on the base specificity of the calicheamicin aminopentosyltransferase CalG4, provides growing support for the calicheamicin aminopentose pathway as a TDP-sugar-dependent process.

Indexed as

Amino Acid SequenceCarbohydrate SequenceCrystallography, X-RayGlucose 1-DehydrogenaseKineticsModels, MolecularMolecular Sequence DataPentosesProtein ConformationSequence Homology, Amino AcidGlucose 1-DehydrogenasePentosesbiosynthesiscalicheamicincarbohydratecrystal structuredehydrogenasedeoxysugarenediynenatural productsugar nucleotideUDP-glucose dehydrogenase (UGDH)

Identifiers

PMID26240141
PMCPMC4646273
OpenAlexW1849990031

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.