1z5c

From Proteopedia

(Difference between revisions)

Revision as of 08:55, 2 May 2018

Topoisomerase VI-B, ADP Pi bound dimer form

Structural highlights

1z5c is a 2 chain structure with sequence from 'saccharolobus shibatae'. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
NonStd Res:
Related:	1mu5, 1mx0, 1z59, 1z5a, 1z5b
Gene:	top6B ('Saccharolobus shibatae')
Activity:	DNA topoisomerase (ATP-hydrolyzing), with EC number 5.99.1.3
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[TOP6B_SULSH] Relaxes both positive and negative superturns and exhibits a strong decatenase activity.[HAMAP-Rule:MF_00322]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

GHL proteins are functionally diverse enzymes defined by the presence of a conserved ATPase domain that self-associates to trap substrate upon nucleotide binding. The structural states adopted by these enzymes during nucleotide hydrolysis and product release, and their consequences for enzyme catalysis, have remained unclear. Here, we have determined a complete structural map of the ATP turnover cycle for topoVI-B, the ATPase subunit of the archaeal GHL enzyme topoisomerase VI. With this ensemble of structures, we show that significant conformational changes in the subunit occur first upon ATP binding, and subsequently upon release of hydrolyzed P(i). Together, these data provide a structural framework for understanding the role of ATP hydrolysis in the type II topoisomerase reaction. Our results also suggest that the GHL ATPase module is a molecular switch in which ATP hydrolysis serves as a prerequisite but not a driving force for substrate-dependent structural transitions in the enzyme.

Structural dissection of ATP turnover in the prototypical GHL ATPase TopoVI.,Corbett KD, Berger JM Structure. 2005 Jun;13(6):873-82. PMID:15939019^[1]

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

References

↑ Corbett KD, Berger JM. Structural dissection of ATP turnover in the prototypical GHL ATPase TopoVI. Structure. 2005 Jun;13(6):873-82. PMID:15939019 doi:http://dx.doi.org/10.1016/j.str.2005.03.013

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1z5c"

@@ Line 1: / Line 1: @@
 ==Topoisomerase VI-B, ADP Pi bound dimer form==
 <StructureSection load='1z5c' size='340' side='right' caption='[[1z5c]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1z5c]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_51178 Atcc 51178]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z5C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z5C FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1z5c]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/'saccharolobus_shibatae' 'saccharolobus shibatae']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z5C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z5C FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1mu5|1mu5]], [[1mx0|1mx0]], [[1z59|1z59]], [[1z5a|1z5a]], [[1z5b|1z5b]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">top6B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2286 ATCC 51178])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">top6B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2286 'Saccharolobus shibatae'])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1z5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z5c OCA], [http://pdbe.org/1z5c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z5c RCSB], [http://www.ebi.ac.uk/pdbsum/1z5c PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1z5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z5c OCA], [http://pdbe.org/1z5c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z5c RCSB], [http://www.ebi.ac.uk/pdbsum/1z5c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1z5c ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 16: / Line 17: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z5/1z5c_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z5/1z5c_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1z5c ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 31: / Line 32: @@
 </div>
 <div class="pdbe-citations 1z5c" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Topoisomerase|Topoisomerase]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 51178]]
+[[Category: Saccharolobus shibatae]]
 [[Category: Berger, J M]]
 [[Category: Corbett, K D]]

1z5c

From Proteopedia

Revision as of 08:55, 2 May 2018

Topoisomerase VI-B, ADP Pi bound dimer form

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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