Journal:Acta Cryst D:S2059798320015004
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| - | <StructureSection load='' size='450' side='right' scene=' | + | <StructureSection load='' size='450' side='right' scene='86/869944/Cv/1' caption=''> |
===The substrate binding in the bile acid transporter ASBT<sub>Yf</sub> of ''Yersinia frederiksenii''=== | ===The substrate binding in the bile acid transporter ASBT<sub>Yf</sub> of ''Yersinia frederiksenii''=== | ||
<big>Xiaodong Wang, Ying Lyu, Yujia Ji, Ziyi Sun and Xiaoming Zhou</big> <ref>doi: 10.1107/S2059798320015004</ref> | <big>Xiaodong Wang, Ying Lyu, Yujia Ji, Ziyi Sun and Xiaoming Zhou</big> <ref>doi: 10.1107/S2059798320015004</ref> | ||
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In this study, four structures of an ASBT protein, called ASBT<sub>Yf</sub>, are determined. In these structures, several ligand-like acid molecules, including a citrate, a glycine and a sulfate, bind in a putative substrate-binding pocket of the protein. The structural data are consistent with a computational model the defines the substrate-binding site, and support the binding pattern of bile acids. Functional analysis further validates the computational bile acid binding model, which provides structural insights toward its transport mechanism. | In this study, four structures of an ASBT protein, called ASBT<sub>Yf</sub>, are determined. In these structures, several ligand-like acid molecules, including a citrate, a glycine and a sulfate, bind in a putative substrate-binding pocket of the protein. The structural data are consistent with a computational model the defines the substrate-binding site, and support the binding pattern of bile acids. Functional analysis further validates the computational bile acid binding model, which provides structural insights toward its transport mechanism. | ||
| + | <scene name='86/869944/Cv/3'>The computational docking of TCA</scene> in the PDB entry [[4n7x]]. TCA molecule (cyan stick) docked into the outward-facing central cavity viewed from the extracellular side. <scene name='86/869944/Cv/4'>The docked TCA is consistent with surface electrostatics calculation</scene>. | ||
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| + | Comparison of the outward-facing ASBT<sub>Yf</sub>-Pair1<sub>Linked</sub> and the inward-facing ASBT<sub>Yf</sub>-Pair3<sub>Cit</sub>. TM4 and TM9 are displayed as rocket, and the bound citrate is shown in stick mode. The relative position of Extracellular part is labeled. | ||
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| + | The outward-facing ASBT<sub>Yf</sub>-Pair1<sub>Linked</sub> ([[6lh1]]; teal): | ||
| + | *<scene name='86/869944/Cv/11'>Side view</scene>. | ||
| + | *<scene name='86/869944/Cv/8'>View from the top</scene>. | ||
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| + | The inward-facing ASBT<sub>Yf</sub>-Pair3<sub>Cit</sub> ([[6lgv]]; orange): | ||
| + | *<scene name='86/869944/Cv/10'>Side view</scene>. | ||
| + | *<scene name='86/869944/Cv/12'>View from the bottom</scene>. | ||
| + | These scenes show the example of a ligand-like citrate bound in the substrate-binding site defined by the docking model. More importantly, the citrate binds to similar locations in both outward-facing and inward-facing states, mimicking the binding of bile acids. | ||
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| + | '''PDB references:''' ASBTYf, P10C/S291C mutant, with citrate bound, [[6lgv]]; with glycine bound, [[6lgy]]; with sulfate bound, [[6lgz]]; without acid bound, [[6lh0]]. | ||
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<b>References</b><br> | <b>References</b><br> | ||
<references/> | <references/> | ||
</StructureSection> | </StructureSection> | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
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