ArticleScientific reports2013
Unveiling the gating mechanism of ECF transporter RibU.
Article in Scientific reports, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 12 citations in OpenAlex.
- Identification of inhibitors targeting the energy-coupling factor (ECF) transporters.Communications biology · 2023Article
- An Aromatic Cap Seals the Substrate Binding Site in an ECF-Type S Subunit for Riboflavin.Journal of molecular biology · 2016Article
- Structures of FolT in substrate-bound and substrate-released conformations reveal a gating mechanism for ECF transporters.Nature communications · 2015Article
- ATP-dependent Conformational Changes Trigger Substrate Capture and Release by an ECF-type Biotin Transporter.The Journal of biological chemistry · 2015Article
- Functional loop dynamics of the streptavidin-biotin complex.Scientific reports · 2015Article
- Extensive Identification of Bacterial Riboflavin Transporters and Their Distribution across Bacterial Species.PloS one · 2015Article
- Pyridoxamine is a substrate of the energy-coupling factor transporter HmpT.Cell discovery · 2015Article
- Structural insights into the transport of small molecules across membranes.Current opinion in structural biology · 2014Review
- Structural diversity of ABC transporters.The Journal of general physiology · 2014Review
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Energy-coupling factor (ECF) transporters are responsible for uptake of micronutrients in prokaryotes. The recently reported crystal structure of an ECF transporter RibU provided a foundation for understanding the structure and transport mechanism of ECF transporters. In the present study, molecular dynamics (MD) was carried out to study the conformational changes of the S component RibU upon binding by riboflavin. Our result and analysis revealed a critically important gating mechanism, in which part of loop5 (L5') (eleven residues, missing in the crystal structure) between TM5 and TM6 is dynamically flexible and serves as a gate. Specifically, the L5' opens a large cavity accessible to riboflavin from the extracellular space in Apo-RibU and closes the cavity upon riboflavin binding through hydrophobic packing with riboflavin. Thus, L5'is proposed to be the gate for riboflavin binding. In addition, steered molecular dynamics (SMD) simulation is employed to investigate the translocation dynamics of RibU during riboflavin transport. The simulation result does not show evidence that the S component alone can carry out the transport function. Since loop regions are very flexible and therefore could not be resolved by crystallography, their dynamics are hard to predict based on crystal structure alone.
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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.