3igc

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "3igc" [edit=sysop:move=sysop])
Current revision (07:47, 6 September 2023) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3igc.png|left|200px]]
 
-
<!--
+
==Smallpox virus topoisomerase-DNA transition state==
-
The line below this paragraph, containing "STRUCTURE_3igc", creates the "Structure Box" on the page.
+
<StructureSection load='3igc' size='340' side='right'caption='[[3igc]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[3igc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Variola_virus Variola virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IGC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IGC FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene></td></tr>
-
{{STRUCTURE_3igc| PDB=3igc | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3igc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3igc OCA], [https://pdbe.org/3igc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3igc RCSB], [https://www.ebi.ac.uk/pdbsum/3igc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3igc ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/TOP1_VAR67 TOP1_VAR67] Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at the specific target site 5'-[CT]CCTTp site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(3'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 5'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 5'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity).
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ig/3igc_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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=3igc ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Poxviruses encode their own type IB topoisomerases (TopIBs), which release superhelical tension generated by replication and transcription of their genomes. To investigate the reaction catalyzed by viral TopIBs, we have determined the structure of a variola virus topoisomerase-DNA complex trapped as a vanadate transition state mimic. The structure reveals how the viral TopIB enzymes are likely to position the DNA duplex for ligation following relaxation of supercoils and identifies the sources of friction observed in single-molecule experiments that argue against free rotation. The structure also identifies a conformational change in the leaving group sugar that must occur prior to cleavage and reveals a mechanism for promoting ligation following relaxation of supercoils that involves an Asp-minor groove interaction. Overall, the new structural data support a common catalytic mechanism for the TopIB superfamily but indicate distinct methods for controlling duplex rotation in the small versus large enzyme subfamilies.
-
===Smallpox virus topoisomerase-DNA transition state===
+
Insights from the structure of a smallpox virus topoisomerase-DNA transition state mimic.,Perry K, Hwang Y, Bushman FD, Van Duyne GD Structure. 2010 Jan 13;18(1):127-37. PMID:20152159<ref>PMID:20152159</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_20152159}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 3igc" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 20152159 is the PubMed ID number.
+
-
-->
+
-
{{ABSTRACT_PUBMED_20152159}}
+
-
 
+
-
==About this Structure==
+
-
[[3igc]] is a 4 chain structure of [[Topoisomerase]] with sequence from [http://en.wikipedia.org/wiki/Variola_virus Variola virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IGC OCA].
+
==See Also==
==See Also==
-
*[[Topoisomerase]]
+
*[[Topoisomerase 3D structures|Topoisomerase 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:20152159</ref><references group="xtra"/>
+
__TOC__
-
[[Category: DNA topoisomerase]]
+
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Variola virus]]
[[Category: Variola virus]]
-
[[Category: Bushman, F D.]]
+
[[Category: Bushman FD]]
-
[[Category: Duyne, G D.Van.]]
+
[[Category: Hwang Y]]
-
[[Category: Hwang, Y.]]
+
[[Category: Perry K]]
-
[[Category: Perry, K.]]
+
[[Category: Van Duyne GD]]
-
[[Category: Atp-binding]]
+
-
[[Category: Dna-binding]]
+
-
[[Category: Isomerase]]
+
-
[[Category: Isomerase-dna complex]]
+
-
[[Category: Late protein]]
+
-
[[Category: Nucleotide-binding]]
+
-
[[Category: Poxvirus]]
+
-
[[Category: Protein-dna complex]]
+
-
[[Category: Topoisomerase]]
+

Current revision

Smallpox virus topoisomerase-DNA transition state

PDB ID 3igc

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/3igc"
Personal tools