This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3t6l

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:19, 14 March 2024) (edit) (undo)
 
(3 intermediate revisions not shown.)
Line 1: Line 1:
==Y54F mutant of core streptavidin==
==Y54F mutant of core streptavidin==
-
<StructureSection load='3t6l' size='340' side='right' caption='[[3t6l]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
+
<StructureSection load='3t6l' size='340' side='right'caption='[[3t6l]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3t6l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/As_4.1583 As 4.1583]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T6L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T6L FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3t6l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_avidinii Streptomyces avidinii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T6L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T6L FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3t6f|3t6f]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3t6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t6l OCA], [http://pdbe.org/3t6l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3t6l RCSB], [http://www.ebi.ac.uk/pdbsum/3t6l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3t6l ProSAT]</span></td></tr>
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3t6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t6l OCA], [https://pdbe.org/3t6l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t6l RCSB], [https://www.ebi.ac.uk/pdbsum/3t6l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t6l ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/SAV_STRAV SAV_STRAV]] The biological function of streptavidin is not known. Forms a strong non-covalent specific complex with biotin (one molecule of biotin per subunit of streptavidin).
+
[https://www.uniprot.org/uniprot/SAV_STRAV SAV_STRAV] The biological function of streptavidin is not known. Forms a strong non-covalent specific complex with biotin (one molecule of biotin per subunit of streptavidin).
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
We report a point mutation in the second contact shell of the high-affinity streptavidin-biotin complex that appears to reduce binding affinity through transmitted effects on equilibrium dynamics. The Y54F streptavidin mutation causes a 75-fold loss of binding affinity with 73-fold faster dissociation, a large loss of binding enthalpy (DeltaDeltaH, 3.4 kcal/mol at 37 masculineC) and a small gain in binding entropy (TDeltaDeltaS, 0.7 kcal/mol). The removed Y54 hydroxyl is replaced by a water molecule in the bound structure, but there are no observable changes in structure in the first contact shell and no additional changes surrounding the mutation. Molecular dynamics simulations reveal a large increase in atomic fluctuations for W79, a key biotin contact residue, compared to the wild type complex. The increased W79 fluctuations are caused by loss of water-mediated hydrogen bonds between the Y54 hydroxyl group and peptide backbone atoms in and near W79. We propose that the increased fluctuations diminish the integrity of the W79-biotin interaction and represent a loosening of the "tryptophan collar" which is critical to the slow dissociation and high affinity of streptavidin-biotin binding. These results illustrate how changes in protein dynamics distal to the ligand binding pocket can have a profound impact on ligand binding, even when equilibrium structure is unperturbed.
+
-
 
+
-
Second Contact Shell Mutation Diminishes Streptavidin-Biotin Binding Affinity Through Transmitted Effects on Equilibrium Dynamics.,Baugh L, Le Trong I, Cerutti DS, Mehta N, Gulich S, Stayton PS, Stenkamp RE, Lybrand TP Biochemistry. 2011 Dec 6. PMID:22145986<ref>PMID:22145986</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3t6l" style="background-color:#fffaf0;"></div>
+
==See Also==
==See Also==
-
*[[Avidin|Avidin]]
+
*[[Avidin 3D structures|Avidin 3D structures]]
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: As 4 1583]]
+
[[Category: Large Structures]]
-
[[Category: Baugh, L]]
+
[[Category: Streptomyces avidinii]]
-
[[Category: Lybrand, T P]]
+
[[Category: Baugh L]]
-
[[Category: Stayton, P S]]
+
[[Category: Le Trong I]]
-
[[Category: Stenkamp, R E]]
+
[[Category: Lybrand TP]]
-
[[Category: Trong, I Le]]
+
[[Category: Stayton PS]]
-
[[Category: Biotin binding protein]]
+
[[Category: Stenkamp RE]]

Current revision

Y54F mutant of core streptavidin

PDB ID 3t6l

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3t6l"
Personal tools