6c9w | pdb_00006c9w

Crystal Structure of a ligand bound LacY/Nanobody Complex

spinqualitylabelsall models 6c9w, resolution 3.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6c9w is a 2 chain structure with sequence from Camelus glama and Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: 9PG, BNG Gene: lacY, b0343, JW0334 (ECOLI) Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [LACY_ECOLI] Responsible for transport of beta-galactosides into the cell, with the concomitant import of a proton (symport system). Publication Abstract from PubMed The lactose permease of Escherichia coli (LacY), a dynamic polytopic membrane transport protein, catalyzes galactoside/H(+) symport and operates by an alternating access mechanism that exhibits multiple conformations, the distribution of which is altered by sugar-binding. Camelid nanobodies were made against a double-mutant Gly46 --> Trp/Gly262 --> Trp (LacYWW) that produces an outward-open conformation, as opposed to the cytoplasmic open-state crystal structure of WT LacY. Nanobody 9047 (Nb9047) stabilizes WT LacY in a periplasmic-open conformation. Here, we describe the X-ray crystal structure of a complex between LacYWW, the high-affinity substrate analog 4-nitrophenyl-alpha-d-galactoside (NPG), and Nb9047 at 3-A resolution. The present crystal structure demonstrates that Nb9047 binds to the periplasmic face of LacY, primarily to the C-terminal six-helical bundle, while a flexible loop of the Nb forms a bridge between the N- and C-terminal halves of LacY across the periplasmic vestibule. The bound Nb partially covers the vestibule, yet does not affect the on-rates or off-rates for the substrate binding to LacYWW, which implicates dynamic flexibility of the Nb-LacYWW complex. Nb9047-binding neither changes the overall structure of LacYWW with bound NPG, nor the positions of side chains comprising the galactoside-binding site. The current NPG-bound structure exhibits a more occluded periplasmic vestibule than seen in a previous structure of a (different Nb) apo-LacYWW/Nb9039 complex that we argue is caused by sugar-binding, with major differences located at the periplasmic ends of transmembrane helices in the N-terminal half of LacY. Crystal Structure of a ligand-bound LacY-Nanobody Complex.,Kumar H, Finer-Moore JS, Jiang X, Smirnova I, Kasho V, Pardon E, Steyaert J, Kaback HR, Stroud RM Proc Natl Acad Sci U S A. 2018 Aug 14. pii: 1801774115. doi:, 10.1073/pnas.1801774115. PMID:30108145 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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