ArticlemBio2010
Substrate specificity and structural characteristics of the novel Rieske nonheme iron aromatic ring-hydroxylating oxygenases NidAB and NidA3B3 from Mycobacterium vanbaalenii PYR-1.
Article in mBio, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 21 papers.
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.
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.
Who cites it
21 citing papers in PubMed, 84 citations in OpenAlex.
- Study and Modification of the Polycyclic Aromatic Hydrocarbon Degradation Gene Cluster inMicroorganisms · 2025Article
- Biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons by a novel species of the genusFrontiers in microbiology · 2025Article
- Characterization of a novel aromatic ring-hydroxylating oxygenase, NarA2B2, from thermophilicApplied and environmental microbiology · 2023Article
- Multi-Approach Characterization of Novel Pyrene-DegradingMicroorganisms · 2023Article
- Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach.Environmental microbiome · 2023Article
- Unveiling degradation mechanism of PAHs by amLife · 2022Article
- Comparative Analysis of Bile-Salt Degradation inApplied and environmental microbiology · 2021Article
- Aerobic and Anaerobic Bacterial and Fungal Degradation of Pyrene: Mechanism Pathway Including Biochemical Reaction and Catabolic Genes.International journal of molecular sciences · 2021Review
- Comparative genomic analysis of pyrene-degrading Mycobacterium species: Genomic islands and ring-hydroxylating dioxygenases involved in pyrene degradation.Journal of microbiology (Seoul, Korea) · 2018Article
- Polycyclic Aromatic Hydrocarbon (PAH) Degradation Pathways of the Obligate Marine PAH Degrader Cycloclasticus sp. Strain P1.Applied and environmental microbiology · 2018Article
- Formation of Developmentally Toxic Phenanthrene Metabolite Mixtures by Mycobacterium sp. ELW1.Environmental science & technology · 2017Article
- Effects of Polycyclic Aromatic Hydrocarbon Mixtures on Degradation, Gene Expression, and Metabolite Production in Four Mycobacterium Species.Applied and environmental microbiology · 2016Article
- Use of Substrate-Induced Gene Expression in Metagenomic Analysis of an Aromatic Hydrocarbon-Contaminated Soil.Applied and environmental microbiology · 2016Article
- Current State of Knowledge in Microbial Degradation of Polycyclic Aromatic Hydrocarbons (PAHs): A Review.Frontiers in microbiology · 2016Review
- Dynamic Response of Mycobacterium vanbaalenii PYR-1 to BP Deepwater Horizon Crude Oil.Applied and environmental microbiology · 2015Article
- Abundance and diversity of functional genes involved in the degradation of aromatic hydrocarbons in Antarctic soils and sediments around Syowa Station.Environmental science and pollution research international · 2015Article
- Comparative functional pan-genome analyses to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon metabolism in the genus Mycobacterium.BMC evolutionary biology · 2015Article
- Characterization of novel polycyclic aromatic hydrocarbon dioxygenases from the bacterial metagenomic DNA of a contaminated soil.Applied and environmental microbiology · 2014Article
- Pleiotropic and epistatic behavior of a ring-hydroxylating oxygenase system in the polycyclic aromatic hydrocarbon metabolic network from Mycobacterium vanbaalenii PYR-1.Journal of bacteriology · 2014Article
- Functional robustness of a polycyclic aromatic hydrocarbon metabolic network examined in a nidA aromatic ring-hydroxylating oxygenase mutant of Mycobacterium vanbaalenii PYR-1.Applied and environmental microbiology · 2012Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Rieske nonheme iron aromatic ring-hydroxylating oxygenases (RHOs) NidAB and NidA3B3 from Mycobacterium vanbaalenii PYR-1 have been implicated in the initial oxidation of high-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs), forming cis-dihydrodiols. To clarify how these two RHOs are functionally different with respect to the degradation of HMW PAHs, we investigated their substrate specificities to 13 representative aromatic substrates (toluene, m-xylene, phthalate, biphenyl, naphthalene, phenanthrene, anthracene, fluoranthene, pyrene, benz[a]anthracene, benzo[a]pyrene, carbazole, and dibenzothiophene) by enzyme reconstitution studies of Escherichia coli. Both Nid systems were identified to be compatible with type V electron transport chain (ETC) components, consisting of a [3Fe-4S]-type ferredoxin and a glutathione reductase (GR)-type reductase. Metabolite profiles indicated that the Nid systems oxidize a wide range of aromatic hydrocarbon compounds, producing various isomeric dihydrodiol and phenolic compounds. NidAB and NidA3B3 showed the highest conversion rates for pyrene and fluoranthene, respectively, with high product regiospecificity, whereas other aromatic substrates were converted at relatively low regiospecificity. Structural characteristics of the active sites of the Nid systems were investigated and compared to those of other RHOs. The NidAB and NidA3B3 systems showed the largest substrate-binding pockets in the active sites, which satisfies spatial requirements for accepting HMW PAHs. Spatially conserved aromatic amino acids, Phe-Phe-Phe, in the substrate-binding pockets of the Nid systems appeared to play an important role in keeping aromatic substrates within the reactive distance from the iron atom, which allows each oxygen to attack the neighboring carbons.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.