ArticleThe journal of physical chemistry. B2015
Computational analysis of ammonia transfer along two intramolecular tunnels in Staphylococcus aureus glutamine-dependent amidotransferase (GatCAB).
Article in The journal of physical chemistry. B, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Catalytic Mechanism of the Bacterial Non-Heme Fe(II) and 2-Oxoglutarate Dependent Enzyme AlkB with Single-Stranded DNA Containing Complex Guanine Adducts.Inorganic chemistry · 2025Article
- Impact of a Cancer-Associated Mutation on Poly(ADP-ribose) Polymerase1 Inhibition.The journal of physical chemistry. B · 2025Article
- 3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase.Nature communications · 2024Article
- Impact of a Cancer-Associated Mutation on Poly(ADP-ribose) Polymerase1 Inhibition.bioRxiv : the preprint server for biology · 2024Article
- Structural Basis for Long Residence Time c-Src Antagonist: Insights from Molecular Dynamics Simulations.International journal of molecular sciences · 2024Article
- Effects of Clinical Mutations in the Second Coordination Sphere and Remote Regions on the Catalytic Mechanism of Non-Heme Fe(II)/2-Oxoglutarate-Dependent Aspartyl Hydroxylase AspH.Chemphyschem : a European journal of chemical physics and physical chemistry · 2024Article
- 3D Variability Analysis Reveals a Hidden Conformational Change Controlling Ammonia Transport in Human Asparagine Synthetase.bioRxiv : the preprint server for biology · 2024Article
- Unusual catalytic strategy by non-heme Fe(ii)/2-oxoglutarate-dependent aspartyl hydroxylase AspH.Chemical science · 2024Article
- Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions.Journal of chemical theory and computation · 2023Article
- Investigation of the Inhibition Mechanism of Xanthine Oxidoreductase by Oxipurinol: A Computational Study.Journal of chemical information and modeling · 2023Article
- Computational Characterization of the Inhibition Mechanism of Xanthine Oxidoreductase by Topiroxostat.ACS catalysis · 2023Article
- Single-nucleotide polymorphism of the DNA cytosine deaminase APOBEC3H haplotype I leads to enzyme destabilization and correlates with lung cancer.NAR cancer · 2020Article
- Computational Investigation of APOBEC3H Substrate Orientation and Selectivity.The journal of physical chemistry. B · 2020Article
- Selectivity and Promiscuity in TET-Mediated Oxidation of 5-Methylcytosine in DNA and RNA.Biochemistry · 2019Article
- Comparison of DNA and RNA substrate effects on TET2 structure.Advances in protein chemistry and structural biology · 2019Article
- Insight into wild-type and T1372E TET2-mediated 5hmC oxidation usingChemical science · 2018Article
- Computational investigation of OChemical science · 2017Article
- Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine.Nature chemical biology · 2017Article
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2 authors.
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Abstract
Most bacteria and all archaea misacylate the tRNAs corresponding to Asn and Gln with Asp and Glu (Asp-tRNA(Asn) and Glu-tRNA(Gln)).The GatCAB enzyme of most bacteria converts misacylated Glu-tRNA(Gln) to Gln-tRNA(Gln) in order to enable the incorporation of glutamine during protein synthesis. The conversion process involves the intramolecular transfer of ammonia between two spatially separated active sites. This study presents a computational analysis of the two putative intramolecular tunnels that have been suggested to describe the ammonia transfer between the two active sites. Molecular dynamics simulations have been performed for wild-type GatCAB of S. aureus and its mutants: T175(A)V, K88(B)R, E125(B)D, and E125(B)Q. The two tunnels have been analyzed in terms of free energy of ammonia transfer along them. The probability of occurrence of each type of tunnel and the variation of the probability for wild-type GatCAB and its mutants is also discussed.
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