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.


3tcj

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:23, 14 March 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='3tcj' size='340' side='right'caption='[[3tcj]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
<StructureSection load='3tcj' size='340' side='right'caption='[[3tcj]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3tcj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"achromobacter_fischeri"_(beijerinck_1889)_bergey_et_al._1930 "achromobacter fischeri" (beijerinck 1889) bergey et al. 1930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TCJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TCJ FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3tcj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aliivibrio_fischeri Aliivibrio fischeri] and [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TCJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TCJ FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</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]] 1.93&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3jrz|3jrz]], [[3jsc|3jsc]], [[3ku8|3ku8]], [[3kua|3kua]], [[3hpw|3hpw]], [[3g7f|3g7f]]</div></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ccdB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=668 "Achromobacter fischeri" (Beijerinck 1889) Bergey et al. 1930])</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=3tcj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tcj OCA], [https://pdbe.org/3tcj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tcj RCSB], [https://www.ebi.ac.uk/pdbsum/3tcj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tcj 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=3tcj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tcj OCA], [https://pdbe.org/3tcj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tcj RCSB], [https://www.ebi.ac.uk/pdbsum/3tcj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tcj ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[https://www.uniprot.org/uniprot/CCDA_ECO57 CCDA_ECO57]] Antitoxin component of a toxin-antitoxin (TA) module which inhibits the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Binds to and blocks the activity of CcdB; will also remove bound CcdB protein from the CcdB-GyrA complex by forming a CcdA-CcdB complex, a process termed rejuvenation. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdB (By similarity).
+
[https://www.uniprot.org/uniprot/Q84B82_ALIFS Q84B82_ALIFS]
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
Intrinsically disordered proteins (IDPs) are proteins that lack a unique three-dimensional structure in their native state. Many have, however, been found to fold into a defined structure when interacting with specific binding partners. The energetic implications of such behavior have been widely discussed, yet experimental thermodynamic data is scarce. We present here a thorough thermodynamic and structural study of the binding of an IDP (antitoxin CcdA) to its molecular target (gyrase poison CcdB). We show that the binding-coupled folding of CcdA is driven by a combination of specific intramolecular interactions that favor the final folded structure and a less specific set of intermolecular contacts that provide a desolvation entropy boost. The folded structure of the bound IDP appears to be defined largely by its own amino acid sequence, with the binding partner functioning more as a facilitator than a mold to conform to. On the other hand, specific intermolecular interactions do increase the binding affinity up to the picomolar range. Overall, this study shows how an IDP can achieve very strong and structurally well-defined binding and it provides significant insight into the molecular forces that enable such binding properties.
+
-
 
+
-
Energetic basis of uncoupling folding from binding for an intrinsically disordered protein.,Drobnak I, De Jonge N, Haesaerts S, Vesnaver G, Loris R, Lah J J Am Chem Soc. 2013 Jan 30;135(4):1288-94. doi: 10.1021/ja305081b. Epub 2013 Jan , 16. PMID:23289531<ref>PMID:23289531</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3tcj" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
 +
[[Category: Aliivibrio fischeri]]
 +
[[Category: Escherichia coli O157:H7]]
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Jonge, N De]]
+
[[Category: De Jonge N]]
-
[[Category: Loris, R]]
+
[[Category: Loris R]]
-
[[Category: Alpha+beta sh3 domain intrinsically disordered]]
+
-
[[Category: Toxin-antitoxin complex]]
+

Current revision

CcdB dimer from V. fisheri in complex with one C-terminal domain of F-plasmid CcdA

PDB ID 3tcj

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/3tcj"
Personal tools