Evidence map›Paper›PMID 40299693›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2025

Structural basis for substrate selectivity by site-one protease revealed by studies with a small-molecule inhibitor.

Ashley V Bullington, Ilaria Micallo, Bilkish Bajaj, Pankaj Kumar, Netanya Schlamowitz, Aurora Silva, Sebastian Hendrix, Noam Zelcer, Daniel L Kober

Abstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2025. 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
–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

2 citing papers in PubMed.

  1. Article
  2. 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

9 authors.

Ashley V BullingtonDepartment of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390.ORCID 0009-0005-0189-4151
Ilaria MicalloDepartment of Medical Biochemistry, Amsterdam University Medical Centers, location Academic Medical Center, University of Amsterdam, Amsterdam 1105AZ, the Netherlands.ORCID 0009-0008-2438-1828
Bilkish BajajDepartment of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390.ORCID 0009-0005-1965-4797
Pankaj KumarDepartment of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390.ORCID 0000-0002-7025-5530
Netanya SchlamowitzDepartment of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390.ORCID 0009-0000-4098-2334
Aurora SilvaDepartment of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390.ORCID 0009-0001-9758-3454
Sebastian HendrixDepartment of Medical Biochemistry, Amsterdam University Medical Centers, location Academic Medical Center, University of Amsterdam, Amsterdam 1105AZ, the Netherlands.ORCID 0000-0003-2055-9883
Noam ZelcerDepartment of Medical Biochemistry, Amsterdam University Medical Centers, location Academic Medical Center, University of Amsterdam, Amsterdam 1105AZ, the Netherlands.ORCID 0000-0001-6935-7532
Daniel L KoberDepartment of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390.ORCID 0000-0001-8657-9348

Funding

UT Southwestern NORCP30DK127984 · NIDDK · UT SOUTHWESTERN MEDICAL CENTER · PI Jeffrey M Zigman · 2022 to 2026
$7.4M
Structural and mechanistic basis for the maturation of site-one protease in the secretory pathwayR01GM155152 · NIGMS · UT SOUTHWESTERN MEDICAL CENTER · PI Daniel Luke Kober · 2024 to 2026
$1.0M
The mechanistic basis for targeted protein degradation in lipid metabolismR00GM141261 · NIGMS · UT SOUTHWESTERN MEDICAL CENTER · PI KOBER, DANIEL LUKE · 2023 to 2025
$747k
Dutch Heart Foundation 2013T111HHS | NIH | National Institute of General Medical Sciences (NIGMS) R00GM141261HHS | NIH | National Institute of General Medical Sciences (NIGMS) R01GM155152Netherlands Organization for Scientific Research 016.176.643Netherlands Organization for Scientific Research M.22.034; GENESISNIDDK NIH HHS P30 DK127984NIGMS NIH HHS R00 GM141261NIGMS NIH HHS R01 GM155152
6 · The paper itself

Abstract

Site-one protease (S1P) carries out the first proteolytic step to activate membrane-bound effector proteins in the Golgi. S1P matures through an autocatalytic process that begins in the endoplasmic reticulum (ER) and culminates with the displacement of its inhibitory pro-domain by its cofactor, sterol regulatory element binding protein-regulating gene (SPRING). Spatial control of S1P activity and substrate localization underpins signaling pathways governing, among others, lipogenesis, ER stress, and lysosome biogenesis. The factors governing these pathways are activated by S1P-mediated proteolysis upon their regulated transport from the ER to the Golgi. S1P cleaves substrates with the recognition sequence RX(L/I/V)Z, where X is any residue other than Cys or Pro and Z is preferably Leu or Lys. However, the structural basis for substrate recognition by S1P has remained unknown. Here, we used the small molecule PF-429242, a competitive inhibitor of S1P, to investigate substrate recognition by the S1P/SPRING complex. We determined the structure of S1P/SPRING bound to PF-429242 and found that PF-429242 binds S1P in the same pocket that recognizes the substrate's conserved P

Indexed as

Proprotein ConvertasesSerine EndopeptidasesCrystallography, X-RayEndoplasmic ReticulumHumansModels, MolecularProtein BindingProteolysisSubstrate Specificitymembrane-bound transcription factor peptidase, site 1Proprotein ConvertasesSerine Endopeptidasescholesterolcryo-EMproteasessite-1-proteaseSPRING

Identifiers

PMID40299693
PMCPMC12067269

What OpenQuestion holds

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Registered trials

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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.