5wo2

From Proteopedia

(Difference between revisions)

Current revision

Chaperone Spy bound to Casein Fragment (Casein un-modeled)

Structural highlights

5wo2 is a 2 chain structure with sequence from Escherichia coli. This structure supersedes the now removed PDB entry 5iog. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.769Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SPY_ECOLI An ATP-independent periplasmic chaperone, decreases protein aggregation and helps protein refolding. Binds substrate over a large region of its convex inner surface (PubMed:21317898, PubMed:24497545). Substrate protein folds while it is bound to chaperone (PubMed:26619265). Increasing Spy flexibility increases its substrate affinity and overall chaperone activity (shown for 3 different substrates) (PubMed:24497545). Protects proteins in vitro against tannin inactivation; tannins have antimicrobial activity (PubMed:21317898). Overexpression enhances the stability of otherwise unstable periplasmic proteins (PubMed:21317898).^[1] ^[2] ^[3]

Publication Abstract from PubMed

Challenges in determining the structures of heterogeneous and dynamic protein complexes have greatly hampered past efforts to obtain a mechanistic understanding of many important biological processes. One such process is chaperone-assisted protein folding. Obtaining structural ensembles of chaperone-substrate complexes would ultimately reveal how chaperones help proteins fold into their native state. To address this problem, we devised a new structural biology approach based on X-ray crystallography, termed residual electron and anomalous density (READ). READ enabled us to visualize even sparsely populated conformations of the substrate protein immunity protein 7 (Im7) in complex with the Escherichia coli chaperone Spy, and to capture a series of snapshots depicting the various folding states of Im7 bound to Spy. The ensemble shows that Spy-associated Im7 samples conformations ranging from unfolded to partially folded to native-like states and reveals how a substrate can explore its folding landscape while being bound to a chaperone.

Visualizing chaperone-assisted protein folding.,Horowitz S, Salmon L, Koldewey P, Ahlstrom LS, Martin R, Quan S, Afonine PV, van den Bedem H, Wang L, Xu Q, Trievel RC, Brooks CL 3rd, Bardwell JC Nat Struct Mol Biol. 2016 May 30. doi: 10.1038/nsmb.3237. PMID:27239796^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Quan S, Koldewey P, Tapley T, Kirsch N, Ruane KM, Pfizenmaier J, Shi R, Hofmann S, Foit L, Ren G, Jakob U, Xu Z, Cygler M, Bardwell JC. Genetic selection designed to stabilize proteins uncovers a chaperone called Spy. Nat Struct Mol Biol. 2011 Feb 13. PMID:21317898 doi:10.1038/nsmb.2016
↑ Quan S, Wang L, Petrotchenko EV, Makepeace KA, Horowitz S, Yang J, Zhang Y, Borchers CH, Bardwell JC. Super Spy variants implicate flexibility in chaperone action. Elife. 2014;3:e01584. doi: 10.7554/eLife.01584. Epub 2014 Feb 4. PMID:24497545 doi:http://dx.doi.org/10.7554/eLife.01584
↑ Stull F, Koldewey P, Humes JR, Radford SE, Bardwell JC. Substrate protein folds while it is bound to the ATP-independent chaperone Spy. Nat Struct Mol Biol. 2016 Jan;23(1):53-8. doi: 10.1038/nsmb.3133. Epub 2015 Nov, 30. PMID:26619265 doi:http://dx.doi.org/10.1038/nsmb.3133
↑ Horowitz S, Salmon L, Koldewey P, Ahlstrom LS, Martin R, Quan S, Afonine PV, van den Bedem H, Wang L, Xu Q, Trievel RC, Brooks CL 3rd, Bardwell JC. Visualizing chaperone-assisted protein folding. Nat Struct Mol Biol. 2016 May 30. doi: 10.1038/nsmb.3237. PMID:27239796 doi:http://dx.doi.org/10.1038/nsmb.3237

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5wo2"

@@ Line 3: / Line 3: @@
 <StructureSection load='5wo2' size='340' side='right'caption='[[5wo2]], [[Resolution|resolution]] 1.77&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5wo2]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5iog 5iog]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WO2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5WO2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5wo2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5iog 5iog]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WO2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WO2 FirstGlance]. <br>
-</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=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.769&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5iog|5iog]]</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=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5wo2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wo2 OCA], [http://pdbe.org/5wo2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wo2 RCSB], [http://www.ebi.ac.uk/pdbsum/5wo2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wo2 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=5wo2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wo2 OCA], [https://pdbe.org/5wo2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wo2 RCSB], [https://www.ebi.ac.uk/pdbsum/5wo2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wo2 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SPY_ECOLI SPY_ECOLI]] An ATP-independent periplasmic chaperone, decreases protein aggregation and helps protein refolding. Binds substrate over a large region of its convex inner surface (PubMed:21317898, PubMed:24497545). Substrate protein folds while it is bound to chaperone (PubMed:26619265). Increasing Spy flexibility increases its substrate affinity and overall chaperone activity (shown for 3 different substrates) (PubMed:24497545). Protects proteins in vitro against tannin inactivation; tannins have antimicrobial activity (PubMed:21317898). Overexpression enhances the stability of otherwise unstable periplasmic proteins (PubMed:21317898).<ref>PMID:21317898</ref> <ref>PMID:24497545</ref> <ref>PMID:26619265</ref>
+[https://www.uniprot.org/uniprot/SPY_ECOLI SPY_ECOLI] An ATP-independent periplasmic chaperone, decreases protein aggregation and helps protein refolding. Binds substrate over a large region of its convex inner surface (PubMed:21317898, PubMed:24497545). Substrate protein folds while it is bound to chaperone (PubMed:26619265). Increasing Spy flexibility increases its substrate affinity and overall chaperone activity (shown for 3 different substrates) (PubMed:24497545). Protects proteins in vitro against tannin inactivation; tannins have antimicrobial activity (PubMed:21317898). Overexpression enhances the stability of otherwise unstable periplasmic proteins (PubMed:21317898).<ref>PMID:21317898</ref> <ref>PMID:24497545</ref> <ref>PMID:26619265</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Bardwell, J C.A]]
+[[Category: Bardwell JCA]]
-[[Category: Horowitz, S]]
+[[Category: Horowitz S]]
-[[Category: Koldewey, P]]
+[[Category: Koldewey P]]
-[[Category: Martin, R]]
+[[Category: Martin R]]
-[[Category: Chaperone]]

5wo2

From Proteopedia

Current revision

Chaperone Spy bound to Casein Fragment (Casein un-modeled)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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