3oiy: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3oiy.jpg|left|200px]]
-<!--
+==Helicase domain of reverse gyrase from Thermotoga maritima==
-The line below this paragraph, containing "STRUCTURE_3oiy", creates the "Structure Box" on the page.
+<StructureSection load='3oiy' size='340' side='right'caption='[[3oiy]], [[Resolution|resolution]] 2.35&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'>[[3oiy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OIY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OIY 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]] 2.35&#8491;</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=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>
-{{STRUCTURE_3oiy|  PDB=3oiy  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3oiy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oiy OCA], [https://pdbe.org/3oiy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oiy RCSB], [https://www.ebi.ac.uk/pdbsum/3oiy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oiy ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Reverse gyrase is the only topoisomerase that can introduce positive supercoils into DNA in an ATP-dependent process. It has a modular structure and harnesses a helicase-like domain to support a topoisomerase activity, thereby creating the unique function of positive DNA supercoiling. The isolated topoisomerase domain can relax negatively supercoiled DNA, an activity that is suppressed in reverse gyrase. The isolated helicase-like domain is a nucleotide-dependent switch that is attenuated by the topoisomerase domain. Inter-domain communication thus appears central for the functional cooperation of the two domains. The latch, an insertion into the helicase-like domain, has been suggested as an important element in coordinating their activities. Here, we have dissected the influence of the latch on nucleotide and DNA binding to the helicase-like domain, and on DNA supercoiling by reverse gyrase. We find that the latch is required for positive DNA supercoiling. It is crucial for the cooperativity of DNA and nucleotide binding to the helicase-like domain. The latch contributes to DNA binding, and affects the preference of reverse gyrase for ssDNA. Thus, the latch coordinates the individual domain activities by modulating the helicase-like domain, and by communicating changes in the nucleotide state to the topoisomerase domain.
-===Helicase domain of reverse gyrase from Thermotoga maritima===
+The latch modulates nucleotide and DNA binding to the helicase-like domain of Thermotoga maritima reverse gyrase and is required for positive DNA supercoiling.,Ganguly A, Del Toro Duany Y, Rudolph MG, Klostermeier D Nucleic Acids Res. 2010 Nov 4. PMID:21051354<ref>PMID:21051354</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3oiy" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_21051354}}, adds the Publication Abstract to the page
+*[[Gyrase 3D Structures|Gyrase 3D Structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 21051354 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21051354}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-OIY is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OIY OCA].
-==Reference==
-<ref group="xtra">PMID:21051354</ref><references group="xtra"/>
 [[Category: Thermotoga maritima]]
-[[Category: Klostermeier, D.]]
+[[Category: Klostermeier D]]
-[[Category: Rudolph, M G.]]
+[[Category: Rudolph MG]]
-[[Category: Archaea]]
-[[Category: Dna supercoiling]]
-[[Category: Helicase]]
-[[Category: Isomerase]]
-[[Category: Topoisomerase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec  1 11:34:21 2010''