Evidence map›Paper›PMID 29767960›Full record

ArticleBiochemistry2018

Comparison of Alicyclobacillus acidocaldarius o-Succinylbenzoate Synthase to Its Promiscuous N-Succinylamino Acid Racemase/ o-Succinylbenzoate Synthase Relatives.

Denis Odokonyero, Andrew W McMillan, Udupi A Ramagopal, Rafael Toro, Dat P Truong, Mingzhao Zhu, Mariana S Lopez, Belema Somiari, Meghann Herman, Asma Aziz and 6 more

Open access · greenAbstract readComparative Study
In one paragraph

Article in Biochemistry, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
0.8field-weighted citation impact, top 32% 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

4 citing papers in PubMed, 10 citations in OpenAlex.

  1. Article
  2. Article
  3. Review
  4. 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

16 authors at 5 institutions in 2 countries.

Denis OdokonyeroDepartment of Biochemistry and Biophysics , Texas A&M University , 2128 TAMU , College Station , Texas 77843-2128 , United States.
Andrew W McMillanDepartment of Biochemistry and Biophysics , Texas A&M University , 2128 TAMU , College Station , Texas 77843-2128 , United States.ORCID 0000-0002-8005-5225
Udupi A RamagopalPoornaprajna Institute , Bangalore , India.ORCID 0000-0003-1045-9838
Rafael Toro
Dat P TruongDepartment of Biochemistry and Biophysics , Texas A&M University , 2128 TAMU , College Station , Texas 77843-2128 , United States.
Mingzhao ZhuCPRIT Synthesis and Drug-Lead Discovery Lab, Department of Chemistry and Biochemistry , Baylor University , One Bear Place , Waco , Texas 76798-7348 , United States.
Mariana S LopezDepartment of Biochemistry and Biophysics , Texas A&M University , 2128 TAMU , College Station , Texas 77843-2128 , United States.
Belema SomiariDepartment of Biochemistry and Biophysics , Texas A&M University , 2128 TAMU , College Station , Texas 77843-2128 , United States.
Meghann HermanDepartment of Biochemistry and Biophysics , Texas A&M University , 2128 TAMU , College Station , Texas 77843-2128 , United States.
Asma AzizDepartment of Biochemistry and Biophysics , Texas A&M University , 2128 TAMU , College Station , Texas 77843-2128 , United States.
Jeffrey B Bonanno
Kenneth G HullCPRIT Synthesis and Drug-Lead Discovery Lab, Department of Chemistry and Biochemistry , Baylor University , One Bear Place , Waco , Texas 76798-7348 , United States.ORCID 0000-0002-3697-9551
Stephen K BurleyRCSB Protein Data Bank, Institute for Quantitative Biomedicine , Rutgers, The State University of New Jersey , Piscataway , New Jersey 08854-8076 , United States.ORCID 0000-0002-2487-9713
Daniel RomoCPRIT Synthesis and Drug-Lead Discovery Lab, Department of Chemistry and Biochemistry , Baylor University , One Bear Place , Waco , Texas 76798-7348 , United States.ORCID 0000-0003-3805-092X
Steven C Almo
Margaret E GlasnerDepartment of Biochemistry and Biophysics , Texas A&M University , 2128 TAMU , College Station , Texas 77843-2128 , United States.ORCID 0000-0003-1818-1965
Texas A&M University · USAlbert Einstein College of Medicine · USBaylor University · USPoornaprajna Institute of Scientific Research · INRutgers, The State University of New Jersey · US

Funding

SUBPROJECT 5U54GM074945 · NIGMS · SGX PHARMACEUTICALS, INC. · PI BURLEY, STEPHEN KEVIN · 2005 to 2009
$46.2M
The NYSGRC: A Large Scale Center for PSI:BiologyU54GM094662 · NIGMS · ALBERT EINSTEIN COLLEGE OF MEDICINE, INC · PI SEIDEL, RONALD D · 2010 to 2014
$32.6M
Case Center for Synchrotron BiosciencesP30EB009998 · NIBIB · CASE WESTERN RESERVE UNIVERSITY · PI CHANCE, MARK R · 2009 to 2018
$8.4M
NIBIB NIH HHS P30 EB009998NIGMS NIH HHS U54 GM074945NIGMS NIH HHS U54 GM094662
6 · The paper itself

Abstract

Studying the evolution of catalytically promiscuous enzymes like those from the N-succinylamino acid racemase/ o-succinylbenzoate synthase (NSAR/OSBS) subfamily can reveal mechanisms by which new functions evolve. Some enzymes in this subfamily have only OSBS activity, while others catalyze OSBS and NSAR reactions. We characterized several NSAR/OSBS subfamily enzymes as a step toward determining the structural basis for evolving NSAR activity. Three enzymes were promiscuous, like most other characterized NSAR/OSBS subfamily enzymes. However, Alicyclobacillus acidocaldarius OSBS (AaOSBS) efficiently catalyzes OSBS activity but lacks detectable NSAR activity. Competitive inhibition and molecular modeling show that AaOSBS binds N-succinylphenylglycine with moderate affinity in a site that overlaps its normal substrate. On the basis of possible steric conflicts identified by molecular modeling and sequence conservation within the NSAR/OSBS subfamily, we identified one mutation, Y299I, that increased NSAR activity from undetectable to 1.2 × 10

Indexed as

AlicyclobacillusAmino Acid IsomerasesCarbon-Carbon LyasesCatalytic DomainCrystallography, X-RayEvolution, MolecularModels, MolecularPhylogenyProtein ConformationSubstrate SpecificityAmino Acid IsomerasesCarbon-Carbon Lyaseso-succinylbenzoic acid synthase

Identifiers

PMID29767960
PMCPMC7187728
OpenAlexW2804718935

What OpenQuestion holds

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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.