Evidence map›Paper›PMID 40596262›Full record

ArticleScientific reports2025

Biochemical and structural characterization of a reactive intermediate deaminase A homolog from Streptococcus sanguinis.

Alexa B Benedict, Adreana I Aquino, Brandi A Buckner, Swarmistha Devi Aribam, Chhandosee Ganguly, Leonard M Thomas, Philip Bourne, Rakhi Rajan, Diana M Downs, Vijayakumar Somalinga

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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.

Alexa B BenedictDepartment of Biological and Biomedical Sciences, Southwestern Oklahoma State University, Weatherford, OK, USA.
Adreana I AquinoDepartment of Biological and Biomedical Sciences, Southwestern Oklahoma State University, Weatherford, OK, USA.
Brandi A BucknerDepartment of Microbiology, University of Georgia, Athens, GA, USA.
Swarmistha Devi AribamDepartment of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA.
Chhandosee GangulyDepartment of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA.
Leonard M ThomasDepartment of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA.
Philip BourneDepartment of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA.
Rakhi RajanDepartment of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA.
Diana M DownsDepartment of Microbiology, University of Georgia, Athens, GA, USA.
Vijayakumar SomalingaDepartment of Biological and Biomedical Sciences, Southwestern Oklahoma State University, Weatherford, OK, USA. vijay.somalinga@swosu.edu.

Funding

Protein Production and Characterization CoreP30GM145423 · NIGMS · UNIVERSITY OF OKLAHOMA · PI ANN H WEST · 2022 to 2026
$6.9M
Rid family members neutralize endogenous metabolic stressorsR01GM095837 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI DOWNS, DIANA M. · 2011 to 2023
$3.7M
T32 Predoctoral Training Grant in GeneticsT32GM142623 · NIGMS · UNIVERSITY OF GEORGIA · PI Kelly A Dyer, Mary Grace Goll · 2022 to 2026
$2.1M
IDeA-NIGMS-NIH P30GM145423NIGMS NIH HHS P30 GM145423NIGMS NIH HHS R01 GM095837NIGMS NIH HHS T32 GM142623NIH HHS 1T32GM142623NIH HHS GM095837NSF DBI-1757720
6 · The paper itself

Abstract

2-Aminoacrylate (2AA) is a short-lived enamine generated as a catalytic intermediate in the dehydration of serine by serine/threonine dehydratase enzymes. 2AA is a metabolic stressor capable of inactivating important pyridoxal phosphate dependent enzymes in a cell. Detoxification of 2AA in a cell is catalyzed by members of the Reactive intermediate deaminase (Rid) family of proteins, which is conserved across all domains of life. We recently identified a RidA homolog, SSA_0809, hereafter SsRidA, in Streptococcus sanguinis with 50% protein sequence identity to a RidA from Salmonella enterica. 2AA deaminase activity assay revealed that SsRidA is capable of enzymatic deamination of 2AA to pyruvate. Furthermore, L-amino acid oxidase assays showed SsRidA has significant activity against several with imino-amino acids similar to the S. enterica RidA. In addition, functional complementation analysis found that SsRidA restored growth of S. enterica ridA mutant in minimal media constituted to increase 2AA stress in the cell. Finally, the crystal structure of SsRidA revealed a homotrimeric protein with active sites at the interface of two interacting monomers. Structure analysis also showed the presence of active site arginine residue along with an active site water molecule implicated in catalysis.

Indexed as

Bacterial ProteinsStreptococcus sanguisAmino Acid SequenceCatalytic DomainCrystallography, X-RayModels, MolecularProtein ConformationBacterial Proteins2-Amino acrylateEnamine deaminaseMetabolic stressRidAStreptococcus sanguinis

Identifiers

PMID40596262
PMCPMC12218379

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.