biostudies-literatureSingh JScience and Engineering Research BoardJamsetji Tata TrustDepartment of BiotechnologyDBT/Wellcome Trust India AllianceWellcome Trust/DBT India Alliance FellowshipWellcome TrustDBT-IISc Partnership Program Phase-II11712-11726https://www.ebi.ac.uk/biostudies/studies/S-EPMC9723500biostudies-literatureUnknown50(20)Initiation factor 3 (IF3) regulates the fidelity of bacterial translation initiation by debarring the use of non-canonical start codons or non-initiator tRNAs and prevents premature docking of the 50S ribosomal subunit to the 30S pre-initiation complex (PIC). The C-terminal domain (CTD) of IF3 can carry out most of the known functions of IF3 and sustain Escherichia coli growth. However, the roles of the N-terminal domain (NTD) have remained unclear. We hypothesized that the interaction between NTD and initiator tRNAfMet (i-tRNA) is essential to coordinate the movement of the two domains during the initiation pathway to ensure fidelity of the process. Here, using atomistic molecular dynamics (MD) simulation, we show that R25A/Q33A/R66A mutations do not impact NTD structure but disrupt its iNucleic acids researchThe initiation factor 3 (IF3) residues interacting with initiator tRNA elbow modulate the fidelity of translation initiation and growth fitness in Escherichia coli.PMC9723500BT/PR13522R(HR)Tata Chairs/2020–854/78BT/PR27952-INF/22/212/2018BT/PR28058EMR/2016/005617IA/I/17/2/503313Mishra RKSingh JAyyub SAHussain TVarshney UfalseThe initiation factor 3 (IF3) residues interacting with initiator tRNA elbow modulate the fidelity of translation initiation and growth fitness in Escherichia coli.Initiation factor 3 (IF3) regulates the fidelity of bacterial translation initiation by debarring the use of non-canonical start codons or non-initiator tRNAs and prevents premature docking of the 50S ribosomal subunit to the 30S pre-initiation complex (PIC). The C-terminal domain (CTD) of IF3 can carry out most of the known functions of IF3 and sustain Escherichia coli growth. However, the roles of the N-terminal domain (NTD) have remained unclear. We hypothesized that the interaction between NTD and initiator tRNAfMet (i-tRNA) is essential to coordinate the movement of the two domains during the initiation pathway to ensure fidelity of the process. Here, using atomistic molecular dynamics (MD) simulation, we show that R25A/Q33A/R66A mutations do not impact NTD structure but disrupt its i2022-01-01T00:00:00Z2022 Nov2026-05-28T00:40:19.659Z2025-04-04T23:36:55.546ZS-EPMC97235003639950910.1093/nar/gkac1053