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Literature DB >> 25654336

Computational analysis of ammonia transfer along two intramolecular tunnels in Staphylococcus aureus glutamine-dependent amidotransferase (GatCAB).

Sajeewa Walimuni Dewage¹, G Andrés Cisneros.

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.

Entities: Chemical Disease Gene Mutation Species

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Year: 2015 PMID： 25654336 PMCID： PMC5639903 DOI： 10.1021/jp5123568

Source DB: PubMed Journal: J Phys Chem B ISSN： 1520-5207 Impact factor: 2.991

33 in total

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Authors: F Massière; M A Badet-Denisot
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6 in total

Computational analysis of ammonia transfer along two intramolecular tunnels in Staphylococcus aureus glutamine-dependent amidotransferase (GatCAB).

1. Electrostatics of nanosystems: application to microtubules and the ribosome.

Review 2. Enzymes with molecular tunnels.

3. The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: understanding from theory and experiment.

Review 4. Computational study of putative residues involved in DNA synthesis fidelity checking in Thermus aquaticus DNA polymerase I.

Review 5. The mechanism of glutamine-dependent amidotransferases.

6. Computational prediction of residues involved in fidelity checking for DNA synthesis in DNA polymerase I.

7. Insight into enzymatic C-F bond formation from QM and QM/MM calculations.

8. Reaction mechanism of the epsilon subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues.

9. Ab initio QM/MM calculations show an intersystem crossing in the hydrogen abstraction step in dealkylation catalyzed by AlkB.

10. MolProbity: all-atom structure validation for macromolecular crystallography.

1. Computational Investigation of APOBEC3H Substrate Orientation and Selectivity.

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3. Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine.

4. Selectivity and Promiscuity in TET-Mediated Oxidation of 5-Methylcytosine in DNA and RNA.

5. Insight into wild-type and T1372E TET2-mediated 5hmC oxidation using ab initio QM/MM calculations.

6. Computational investigation of O₂ diffusion through an intra-molecular tunnel in AlkB; influence of polarization on O₂ transport.