8b01 | pdb_00008b01

Cryo-EM structure of the Tripartite ATP-independent Periplasmic (TRAP) transporter SiaQM from Photobacterium profundum in a nanodisc

spinqualitylabelsall models 8b01, resolution 3.03Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 8b01 is a 3 chain structure with sequence from Helicobacter pylori, Photobacterium profundum SS9 and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: Electron Microscopy, Resolution 3.03Å Ligands: D10, HEX, NA, OCT, PTY, TRD, TWT Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function Q6LPW0_PHOPR Part of the tripartite ATP-independent periplasmic (TRAP) transport system.[RuleBase:RU369079] Publication Abstract from PubMed In bacteria and archaea, tripartite ATP-independent periplasmic (TRAP) transporters uptake essential nutrients. TRAP transporters receive their substrates via a secreted soluble substrate-binding protein. How a sodium ion-driven secondary active transporter is strictly coupled to a substrate-binding protein is poorly understood. Here we report the cryo-EM structure of the sialic acid TRAP transporter SiaQM from Photobacterium profundum at 2.97 A resolution. SiaM comprises a "transport" domain and a "scaffold" domain, with the transport domain consisting of helical hairpins as seen in the sodium ion-coupled elevator transporter VcINDY. The SiaQ protein forms intimate contacts with SiaM to extend the size of the scaffold domain, suggesting that TRAP transporters may operate as monomers, rather than the typically observed oligomers for elevator-type transporters. We identify the Na(+) and sialic acid binding sites in SiaM and demonstrate a strict dependence on the substrate-binding protein SiaP for uptake. We report the SiaP crystal structure that, together with docking studies, suggest the molecular basis for how sialic acid is delivered to the SiaQM transporter complex. We thus propose a model for substrate transport by TRAP proteins, which we describe herein as an 'elevator-with-an-operator' mechanism. Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter.,Davies JS, Currie MJ, North RA, Scalise M, Wright JD, Copping JM, Remus DM, Gulati A, Morado DR, Jamieson SA, Newton-Vesty MC, Abeysekera GS, Ramaswamy S, Friemann R, Wakatsuki S, Allison JR, Indiveri C, Drew D, Mace PD, Dobson RCJ Nat Commun. 2023 Feb 27;14(1):1120. doi: 10.1038/s41467-023-36590-1. PMID:36849793 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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