6c9w: Difference between revisions
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<StructureSection load='6c9w' size='340' side='right'caption='[[6c9w]], [[Resolution|resolution]] 3.00Å' scene=''> | <StructureSection load='6c9w' size='340' side='right'caption='[[6c9w]], [[Resolution|resolution]] 3.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6c9w]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[6c9w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C9W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6C9W FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9PG:4-NITROPHENYL+ALPHA-D-GALACTOPYRANOSIDE'>9PG</scene>, <scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6c9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c9w OCA], [https://pdbe.org/6c9w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6c9w RCSB], [https://www.ebi.ac.uk/pdbsum/6c9w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6c9w ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/LACY_ECOLI LACY_ECOLI] Responsible for transport of beta-galactosides into the cell, with the concomitant import of a proton (symport system). | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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==See Also== | ==See Also== | ||
*[[Antibody 3D structures|Antibody 3D structures]] | |||
*[[Lactose Permease|Lactose Permease]] | *[[Lactose Permease|Lactose Permease]] | ||
== References == | == References == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Escherichia coli K-12]] | ||
[[Category: | [[Category: Lama glama]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Finer-Moore | [[Category: Finer-Moore JS]] | ||
[[Category: Jiang | [[Category: Jiang X]] | ||
[[Category: Kaback | [[Category: Kaback HR]] | ||
[[Category: Kasho | [[Category: Kasho V]] | ||
[[Category: Kumar | [[Category: Kumar H]] | ||
[[Category: Pardon | [[Category: Pardon E]] | ||
[[Category: Smirnova | [[Category: Smirnova I]] | ||
[[Category: Steyaert | [[Category: Steyaert J]] | ||
[[Category: Stroud | [[Category: Stroud RM]] | ||
Latest revision as of 17:59, 4 October 2023
Crystal Structure of a ligand bound LacY/Nanobody ComplexCrystal Structure of a ligand bound LacY/Nanobody Complex
Structural highlights
FunctionLACY_ECOLI Responsible for transport of beta-galactosides into the cell, with the concomitant import of a proton (symport system). Publication Abstract from PubMedThe 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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