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.


2vub

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:24, 21 February 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2vub.gif|left|200px]]
 
-
{{Structure
+
==CCDB, A TOPOISOMERASE POISON FROM E. COLI==
-
|PDB= 2vub |SIZE=350|CAPTION= <scene name='initialview01'>2vub</scene>, resolution 2.45&Aring;
+
<StructureSection load='2vub' size='340' side='right'caption='[[2vub]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=CL:CHLORIDE ION'>CL</scene>
+
<table><tr><td colspan='2'>[[2vub]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VUB FirstGlance]. <br>
-
|ACTIVITY=
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.45&#8491;</td></tr>
-
|GENE= CCDB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></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=2vub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vub OCA], [https://pdbe.org/2vub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vub RCSB], [https://www.ebi.ac.uk/pdbsum/2vub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vub ProSAT]</span></td></tr>
-
 
+
</table>
-
'''CCDB, A TOPOISOMERASE POISON FROM E. COLI'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/CCDB_ECOLI CCDB_ECOLI] Toxic component of a toxin-antitoxin (TA) module, functioning in plasmid maintainence. Responsible for the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Half-life of over 2 hours. Cell killing by CcdB is accompanied by filamentation, defects in chromosome and plasmid segregation, defects in cell division, formation of anucleate cells, decreased DNA synthesis and plasmid loss. Interferes with the activity of DNA gyrase, inducing it to form a covalent GyrA-DNA complex that cannot be resolved, thus promoting breakage of plasmid and chromosomal DNA. DNA breakage requires hydrolyzable ATP. Toxicity is inhibited by labile antitoxin CcdA, which blocks the activity of CcdB; CcdA also removes bound CcdB protein from the CcdB-GyrA complex by forming a CcdA-CcdB complex, a process termed rejuvenation. Also acts to inhibit partitioning of the chromosomal DNA. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdA.<ref>PMID:6327993</ref> <ref>PMID:2651399</ref> <ref>PMID:6308648</ref> <ref>PMID:2615761</ref> <ref>PMID:1324324</ref> <ref>PMID:8604132</ref>
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
The crystal structure of CcdB, a protein that poisons Escherichia coli gyrase, was determined in three crystal forms. The protein consists of a five-stranded antiparallel beta-pleated sheet followed by a C-terminal alpha-helix. In one of the loops of the sheet, a second small three-stranded antiparallel beta-sheet is inserted that sticks out of the molecule as a wing. This wing contains the LysC proteolytic cleavage site that is protected by CcdA and, therefore, forms a likely CcdA recognition site. A dimer is formed by sheet extension and by extensive hydrophobic contacts involving three of the five methionine residues and the C terminus of the alpha-helix. The surface of the dimer on the side of the alpha-helix is overall negatively charged, while the opposite side as well as the wing sheet is dominated by positive charges. We propose that the CcdB dimer binds into the central hole of the 59 kDa N-terminal fragment of GyrA, after disruption of the head dimer interface of GyrA.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vu/2vub_consurf.spt"</scriptWhenChecked>
-
2VUB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VUB OCA].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
Crystal structure of CcdB, a topoisomerase poison from E. coli., Loris R, Dao-Thi MH, Bahassi EM, Van Melderen L, Poortmans F, Liddington R, Couturier M, Wyns L, J Mol Biol. 1999 Jan 29;285(4):1667-77. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9917404 9917404]
+
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2vub ConSurf].
 +
<div style="clear:both"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Bahasi, E M.]]
+
[[Category: Bahasi EM]]
-
[[Category: Couturier, M.]]
+
[[Category: Couturier M]]
-
[[Category: Dao-Thi, M H.]]
+
[[Category: Dao-Thi M-H]]
-
[[Category: Liddington, R.]]
+
[[Category: Liddington R]]
-
[[Category: Loris, R.]]
+
[[Category: Loris R]]
-
[[Category: Melderen, L Van.]]
+
[[Category: Poortmans F]]
-
[[Category: Poortmans, F.]]
+
[[Category: Van Melderen L]]
-
[[Category: Wyns, L.]]
+
[[Category: Wyns L]]
-
[[Category: CL]]
+
-
[[Category: ccdb]]
+
-
[[Category: plasmid]]
+
-
[[Category: topoisomerase poison]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:48:08 2008''
+

Current revision

CCDB, A TOPOISOMERASE POISON FROM E. COLI

PDB ID 2vub

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/2vub"
Personal tools