Evidence map›Paper›PMID 33662397›Full record

ArticleThe Journal of biological chemistry

Structure of 3-mercaptopropionic acid dioxygenase with a substrate analog reveals bidentate substrate binding at the iron center.

Nicholas J York, Molly M Lockart, Sinjinee Sardar, Nimesh Khadka, Wuxian Shi, Ronald E Stenkamp, Jianye Zhang, Philip D Kiser, Brad S Pierce

Open access · goldAbstract read
In one paragraph

Article in The Journal of biological chemistry. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
1.8field-weighted citation impact, top 15% 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

7 citing papers in PubMed, 23 citations in OpenAlex.

  1. Article
  2. Article
  3. Spectroscopic, electrochemical, and kinetic trends in Fe(III)-thiolate disproportionation near physiologic pH.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2024
    Article
  4. Cyanide replaces substrate in obligate-ordered addition of nitric oxide to the non-heme mononuclear iron AvMDO active site.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2023
    Article
  5. Article
  6. Article
  7. Article
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 at 6 institutions in 1 country.

Nicholas J YorkDepartment of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, Alabama, USA.
Molly M LockartDepartment of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, Alabama, USA.
Sinjinee SardarDepartment of Chemistry & Biochemistry, The University of Texas at Arlington, Arlington, Texas, USA.
Nimesh KhadkaDepartment of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA.
Wuxian ShiNational Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, New York, USA.
Ronald E StenkampDepartments of Biological Structure and Biochemistry, University of Washington, Seattle, Washington, USA.
Jianye ZhangDepartment of Ophthalmology, School of Medicine, University of California, Irvine, Irvine, California, USA.
Philip D KiserDepartment of Ophthalmology, School of Medicine, University of California, Irvine, Irvine, California, USA; Department of Physiology & Biophysics, School of Medicine, University of California, Irvine, Irvine, California, USA; Research Service, VA Long Beach Healthcare System, Long Beach, California, USA. Electronic address: pkiser@uci.edu.
Brad S PierceDepartment of Chemistry & Biochemistry, University of Alabama, Tuscaloosa, Alabama, USA. Electronic address: bspierce1@ua.edu.
University of Alabama · USUniversity of California, Irvine · USBrookhaven National Laboratory · USCase Western Reserve University · USThe University of Texas at Arlington · USUniversity of Washington · US

Funding

User Training and OutreachP30GM124165 · NIGMS · CORNELL UNIVERSITY · PI Nozomi Ando, J Christopher Fromme · 2018 to 2026
$34.2M
X-ray Absorption Spectroscopy (XAS) pp.711-759P41GM103393 · NIGMS · STANFORD UNIVERSITY · PI HODGSON, KEITH O · 2012 to 2019
$30.6M
Life Science and Biomedical technology Research center at NSLS-II LSBRP41GM111244 · NIGMS · BROOKHAVEN SCIENCE ASSOC-BROOKHAVEN LAB · PI MCSWEENEY, SEAN · 2014 to 2018
$16.4M
STRUCTURAL STUDIES OF ARRESTINSR01EY009339 · NEI · UNIVERSITY OF WASHINGTON · PI KISER, PHILIP DAVID, PALCZEWSKI, KRZYSZTOF · 1992 to 2025
$16.0M
Pixel Array Detector for Macromolecular CrystallographyS10OD021527 · OD · CORNELL UNIVERSITY · PI EALICK, STEVEN E · 2016 to 2016
$2.0M
Pre-steady state kinetics and O2/NO-reactivity among thiol dioxygenase enzymesR15GM117511 · NIGMS · UNIVERSITY OF TEXAS ARLINGTON · PI PIERCE, BRADLEY S · 2015 to 2023
$1.2M
Retinoid cycles and retinal disease treatmentI01BX004939 · VA · VETERANS HEALTH ADMINISTRATION · PI KISER, PHILIP DAVID · 2020 to 2025
–
BLRD VA I01 BX004939NEI NIH HHS R01 EY009339NIGMS NIH HHS P30 GM124165NIGMS NIH HHS P41 GM103393NIGMS NIH HHS P41 GM111244NIGMS NIH HHS R15 GM117511NIH HHS S10 OD021527
6 · The paper itself

Abstract

Thiol dioxygenases are a subset of nonheme iron oxygenases that catalyze the formation of sulfinic acids from sulfhydryl-containing substrates and dioxygen. Among this class, cysteine dioxygenases (CDOs) and 3-mercaptopropionic acid dioxygenases (3MDOs) are the best characterized, and the mode of substrate binding for CDOs is well understood. However, the manner in which 3-mercaptopropionic acid (3MPA) coordinates to the nonheme iron site in 3MDO remains a matter of debate. A model for bidentate 3MPA coordination at the 3MDO Fe-site has been proposed on the basis of computational docking, whereas steady-state kinetics and EPR spectroscopic measurements suggest a thiolate-only coordination of the substrate. To address this gap in knowledge, we determined the structure of Azobacter vinelandii 3MDO (Av3MDO) in complex with the substrate analog and competitive inhibitor, 3-hydroxypropionic acid (3HPA). The structure together with DFT computational modeling demonstrates that 3HPA and 3MPA associate with iron as chelate complexes with the substrate-carboxylate group forming an additional interaction with Arg168 and the thiol bound at the same position as in CDO. A chloride ligand was bound to iron in the coordination site assigned as the O

Indexed as

3-Mercaptopropionic AcidAzotobacter vinelandiiBacterial ProteinsBinding SitesCatalytic DomainCrystallography, X-RayDioxygenasesIronKineticsModels, MolecularSubstrate Specificity3-Mercaptopropionic AcidBacterial ProteinsDioxygenasesIroncompetitive inhibitioncomputational modelingDFTFT-EPRHYSCOREiron-nitrosylnonheme ironoxygenasestructurethiol dioxygenase

Identifiers

PMID33662397
PMCPMC8050391
OpenAlexW3134944144

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.