6vbg | pdb_00006vbg

Lactose permease complex with thiodigalactoside and nanobody 9043

spinqualitylabelsall models 6vbg, resolution 2.80Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6vbg is a 4 chain structure with sequence from Escherichia coli and Lama glama. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.8Å Ligands: BNG, GAL, YIO 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 structure of lactose permease, stabilized in a periplasmic open conformation by two Gly to Trp replacements (LacYww) and complexed with a nanobody directed against this conformation, provides the highest resolution structure of the symporter. The nanobody binds in a different manner than two other nanobodies made against the same mutant, which also bind to the same general region on the periplasmic side. This region of the protein may represent an immune hotspot. The CDR3 loop of the nanobody is held by hydrogen bonds in a conformation that partially blocks access to the substrate-binding site. As a result, kon and koff for galactoside binding to either LacY or the double mutant complexed with the nanobody are lower than for the other two LacY/nanobody complexes though the Kd values are similar, reflecting the fact that the nanobodies rigidify structures along the pathway. While the wild-type LacY/nanobody complex clearly stabilizes a similar 'extracellular open' conformation in solution, judged by binding kinetics, the complex with wild-type LacY did not yet crystallize, suggesting the nanobody does not bind strongly enough to shift the equilibrium to stabilize a periplasmic side-open conformation suitable for crystallization. However, the similarity of the galactoside binding kinetics for the nanobody-bound complexes with wild type LacY and with LacYWW indicates that they have similar structures, showing that the reported co-structures reliably show nanobody interactions with LacY. Diversity in kinetics correlated with structure in nano body-stabilized LacY.,Kumar H, Finer-Moore J, Smirnova I, Kasho V, Pardon E, Steyaert J, Kaback HR, Stroud RM PLoS One. 2020 May 7;15(5):e0232846. doi: 10.1371/journal.pone.0232846. , eCollection 2020. PMID:32380514 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Lactose Permease

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