Evidence map›Paper›PMID 36941311›Full record

ArticleNature communications2023

Structure and dynamics of the Arabidopsis O-fucosyltransferase SPINDLY.

Shivesh Kumar, Yan Wang, Ye Zhou, Lucas Dillard, Fay-Wei Li, Carly A Sciandra, Ning Sui, Rodolfo Zentella, Emily Zahn, Jeffrey Shabanowitz and 5 more

Open access · goldFull text read
In one paragraph

Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing papers in PubMed
2.2field-weighted citation impact, top 13% 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

9 citing papers in PubMed, 14 citations in OpenAlex.

  1. Article
  2. Article
  3. Review
  4. Review
  5. Article
  6. In silico simulation of glycosylation and related pathways.Analytical and bioanalytical chemistry · 2024
    Review
  7. Article
  8. Article
  9. 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

15 authors at 4 institutions in 1 country.

Shivesh Kumar *Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA.ORCID 0000-0002-3414-4091
Yan Wang *Department of Biology, Duke University, Durham, NC, 27708, USA.ORCID 0000-0003-3262-9930
Ye Zhou *Department of Computer Science, Duke University, Durham, NC, 27705, USA.
Lucas DillardGenome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA.
Fay-Wei LiPlant Biology Section, Cornell University, Ithaca, NY, 14853, USA.ORCID 0000-0002-0076-0152
Carly A SciandraDepartment of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA.
Ning SuiDepartment of Biology, Duke University, Durham, NC, 27708, USA.
Rodolfo ZentellaDepartment of Biology, Duke University, Durham, NC, 27708, USA.ORCID 0000-0003-3986-6250
Emily ZahnDepartment of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA.
Jeffrey ShabanowitzDepartment of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA.ORCID 0000-0001-5750-3539
Donald F HuntDepartment of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA.ORCID 0000-0003-2815-6368
Mario J BorgniaGenome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA.ORCID 0000-0001-9159-1413
Alberto BartesaghiDepartment of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA. alberto.bartesaghi@duke.edu.
Tai-Ping SunDepartment of Biology, Duke University, Durham, NC, 27708, USA. tps@duke.edu.ORCID 0000-0001-5223-2936
Pei ZhouDepartment of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA. peizhou@biochem.duke.edu.ORCID 0000-0002-7823-3416
Duke University · USUniversity of Virginia · USNational Institute of Environmental Health Sciences · USCornell University · US

Funding

PROTEIN SEQUENCING BY TANDEM MASS SPECTROMETRYR01GM037537 · NIGMS · UNIVERSITY OF VIRGINIA CHARLOTTESVILLE · PI HUNT, DONALD F · 1987 to 2023
$17.8M
NIEHS Cryo-EM Core FacilityZICES103326 · NIEHS · NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES · PI BORGNIA, MARIO · 2017 to 2025
$17.0M
Structure and Function Analyses of DELLA Interacting Proteins in ArabidopsisR01GM100051 · NIGMS · DUKE UNIVERSITY · PI SUN, TAI-PING · 2012 to 2021
$2.4M
A Computational Platform for In-Situ Structure Determination at Near-Atomic Resolution using Cryo-Electron TomographyR01GM141223 · NIGMS · DUKE UNIVERSITY · PI BARTESAGHI, ALBERTO · 2021 to 2024
$1.5M
NIGMS NIH HHS R01 GM037537NIGMS NIH HHS R01 GM100051NIGMS NIH HHS R01 GM141223
6 · The paper itself

Abstract

SPINDLY (SPY) in Arabidopsis thaliana is a novel nucleocytoplasmic protein O-fucosyltransferase (POFUT), which regulates diverse developmental processes. Sequence analysis indicates that SPY is distinct from ER-localized POFUTs and contains N-terminal tetratricopeptide repeats (TPRs) and a C-terminal catalytic domain resembling the O-linked-N-acetylglucosamine (GlcNAc) transferases (OGTs). However, the structural feature that determines the distinct enzymatic selectivity of SPY remains unknown. Here we report the cryo-electron microscopy (cryo-EM) structure of SPY and its complex with GDP-fucose, revealing distinct active-site features enabling GDP-fucose instead of UDP-GlcNAc binding. SPY forms an antiparallel dimer instead of the X-shaped dimer in human OGT, and its catalytic domain interconverts among multiple conformations. Analysis of mass spectrometry, co-IP, fucosylation activity, and cryo-EM data further demonstrates that the N-terminal disordered peptide in SPY contains trans auto-fucosylation sites and inhibits the POFUT activity, whereas TPRs 1-5 dynamically regulate SPY activity by interfering with protein substrate binding.

Indexed as

ArabidopsisArabidopsis ProteinsRepressor ProteinsCryoelectron MicroscopyFucoseFucosyltransferasesArabidopsis ProteinsFucoseFucosyltransferasesRepressor ProteinsSPY protein, Arabidopsis

Identifiers

PMID36941311
PMCPMC10027727
OpenAlexW4327941657

What Socratic holds

Textfull text, public
LicenceCC BY
measurements read63
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 Socratic graph.