7ZDF

IF(heme/confined) conformation of CydDC in AMP-PNP(CydD) bound state (Dataset-4)

7ZDF の概要

• エントリーDOI: 10.2210/pdb7zdf/pdb
• 関連するPDBエントリー: 7ZD5
• EMDBエントリー: 14636 14644
• 分子名称: ATP-binding/permease protein CydC, ATP-binding/permease protein CydD, {3,3'-[(9S)-8,13-diethenyl-3,7,12,17-tetramethyl-9,10-dihydroporphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~]dipropanoato(2-)}iron, ... (5 entities in total)
• 機能のキーワード: abc transporter, cyddc, heme transporter, membrane protein
• 由来する生物種: Escherichia coli K-12; 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 129248.72

構造登録者

Wu, D.,Safarian, S. (登録日: 2022-03-29, 公開日: 2023-04-19, 最終更新日: 2023-11-01)

主引用文献

Wu, D.,Mehdipour, A.R.,Finke, F.,Goojani, H.G.,Groh, R.R.,Grund, T.N.,Reichhart, T.M.B.,Zimmermann, R.,Welsch, S.,Bald, D.,Shepherd, M.,Hummer, G.,Safarian, S.
Dissecting the conformational complexity and mechanism of a bacterial heme transporter.
Nat.Chem.Biol., 19:992-1003, 2023

PubMed Abstract: Iron-bound cyclic tetrapyrroles (hemes) are redox-active cofactors in bioenergetic enzymes. However, the mechanisms of heme transport and insertion into respiratory chain complexes remain unclear. Here, we used cellular, biochemical, structural and computational methods to characterize the structure and function of the heterodimeric bacterial ABC transporter CydDC. We provide multi-level evidence that CydDC is a heme transporter required for functional maturation of cytochrome bd, a pharmaceutically relevant drug target. Our systematic single-particle cryogenic-electron microscopy approach combined with atomistic molecular dynamics simulations provides detailed insight into the conformational landscape of CydDC during substrate binding and occlusion. Our simulations reveal that heme binds laterally from the membrane space to the transmembrane region of CydDC, enabled by a highly asymmetrical inward-facing CydDC conformation. During the binding process, heme propionates interact with positively charged residues on the surface and later in the substrate-binding pocket of the transporter, causing the heme orientation to rotate 180°.

PubMed: 37095238
DOI: 10.1038/s41589-023-01314-5

実験手法

ELECTRON MICROSCOPY (2.94 Å)