Evidence map›Paper›PMID 31118236›Full record

ArticleThe Journal of biological chemistry2019

A flap motif in human serine hydroxymethyltransferase is important for structural stabilization, ligand binding, and control of product release.

Sakunrat Ubonprasert, Juthamas Jaroensuk, Wichai Pornthanakasem, Nuntaporn Kamonsutthipaijit, Peerapong Wongpituk, Pitchayathida Mee-Udorn, Thanyada Rungrotmongkol, Onuma Ketchart, Penchit Chitnumsub, Ubolsree Leartsakulpanich and 2 more

Open access · hybridAbstract read
In one paragraph

Article in The Journal of biological chemistry, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed
0.8field-weighted citation impact, top 31% 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

10 citing papers in PubMed, 16 citations in OpenAlex.

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  7. Structural Basis for Allostery in PLP-dependent Enzymes.Frontiers in molecular biosciences · 2022
    Review
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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

12 authors at 7 institutions in 1 country.

Sakunrat UbonprasertFrom the Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
Juthamas JaroensukSchool of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand.
Wichai PornthanakasemBiomolecular Analysis and Application Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), and.ORCID 0000-0002-0265-4927
Nuntaporn KamonsutthipaijitSynchrotron Light Research Institute (Public Organization), Nakhon Ratchasima 30000, Thailand.ORCID 0000-0001-5889-1510
Peerapong WongpitukCenter of Excellence in Computational Chemistry (CECC), Department of Chemistry, and.
Pitchayathida Mee-UdornBioinformatics and Computational Biology Program, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand, and.
Thanyada RungrotmongkolBioinformatics and Computational Biology Program, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand, and.ORCID 0000-0002-7402-3235
Onuma KetchartNational Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathumthani 12120, Thailand.
Penchit ChitnumsubBiomolecular Analysis and Application Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), and.ORCID 0000-0001-5920-3708
Ubolsree LeartsakulpanichBiomolecular Analysis and Application Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), and.ORCID 0000-0002-4011-7217
Pimchai ChaiyenFrom the Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.ORCID 0000-0002-8533-1604
Somchart MaenpuenDepartment of Biochemistry, Faculty of Science, Burapha University, Chonburi 20131, Thailand somchart@go.buu.ac.th.
National Center for Genetic Engineering and Biotechnology · THChulalongkorn University · THMahidol University · THBurapha University · THNational Science and Technology Development Agency · THSynchrotron Light Research Institute · THVidyasirimedhi Institute of Science and Technology · TH

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Human cytosolic serine hydroxymethyltransferase (hcSHMT) is a promising target for anticancer chemotherapy and contains a flexible "flap motif" whose function is yet unknown. Here, using size-exclusion chromatography, analytical ultracentrifugation, small-angle X-ray scattering (SAXS), molecular dynamics (MD) simulations, and ligand-binding and enzyme-kinetic analyses, we studied the functional roles of the flap motif by comparing WT hcSHMT with a flap-deleted variant (hcSHMT/Δflap). We found that deletion of the flap results in a mixture of apo-dimers and holo-tetramers, whereas the WT was mostly in the tetrameric form. MD simulations indicated that the flap stabilizes structural compactness and thereby enhances oligomerization. The hcSHMT/Δflap variant exhibited different catalytic properties in (6

Indexed as

LigandsAmino Acid MotifsBinding SitesEnzyme StabilityGlycine HydroxymethyltransferaseHumansKineticsMolecular Dynamics SimulationMutagenesisProtein BindingProtein MultimerizationProtein Structure, QuaternaryRecombinant ProteinsSubstrate SpecificityTetrahydrofolates5,6,7,8-tetrahydrofolic acidGlycine HydroxymethyltransferaseLigandsRecombinant ProteinsTetrahydrofolatesanalytical ultracentrifugationdTMP synthesis cycleenzyme kineticsflap motif/flexible loopfolatemolecular dynamicsnucleoside/nucleotide biosynthesisoligomerizationPLP-dependent enzymesprotein structurepyridoxal phosphateserine hydroxymethyl transferasesmall-angle X-ray scattering (SAXS)structure-functiontetrahydrofolate-dependent reactions

Identifiers

PMID31118236
PMCPMC6615694
OpenAlexW2946267391

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.