1d3y: Difference between revisions

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New page: left|200px<br /><applet load="1d3y" size="450" color="white" frame="true" align="right" spinBox="true" caption="1d3y, resolution 2.0Å" /> '''STRUCTURE OF THE DNA ...
 
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[[Image:1d3y.gif|left|200px]]<br /><applet load="1d3y" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1d3y, resolution 2.0&Aring;" />
'''STRUCTURE OF THE DNA TOPOISOMERASE VI A SUBUNIT'''<br />


==Overview==
==STRUCTURE OF THE DNA TOPOISOMERASE VI A SUBUNIT==
In all organisms, type II DNA topoisomerases are essential for untangling, chromosomal DNA. We have determined the structure of the DNA-binding core, of the Methanococcus jannaschii DNA topoisomerase VI A subunit at 2.0 A, resolution. The overall structure of this subunit is unique, demonstrating, that archaeal type II enzymes are distinct from other type II, topoisomerases. However, the core structure contains a pair of domains, that are also found in type IA and classic type II topoisomerases., Together, these regions may form the basis of a DNA cleavage mechanism, shared among these enzymes. The core A subunit is a dimer that contains a, deep groove that spans both protomers. The dimer architecture suggests, that DNA is bound in the groove, across the A subunit interface, and that, the two monomers separate during DNA transport. The A subunit of, topoisomerase VI is homologous to the meiotic recombination factor, Spo11, and this structure can serve as a template for probing Spo11 function in, eukaryotes.
<StructureSection load='1d3y' size='340' side='right'caption='[[1d3y]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1d3y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D3Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D3Y FirstGlance]. <br>
</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&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=1d3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d3y OCA], [https://pdbe.org/1d3y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d3y RCSB], [https://www.ebi.ac.uk/pdbsum/1d3y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d3y ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/TOP6A_METJA TOP6A_METJA] Relaxes both positive and negative superturns and exhibits a strong decatenase activity.<ref>PMID:10545127</ref>
== 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/d3/1d3y_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=1d3y ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1D3Y is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii] with NA and MG as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1D3Y OCA].
*[[Topoisomerase 3D structures|Topoisomerase 3D structures]]
 
== References ==
==Reference==
<references/>
Structure and function of an archaeal topoisomerase VI subunit with homology to the meiotic recombination factor Spo11., Nichols MD, DeAngelis K, Keck JL, Berger JM, EMBO J. 1999 Nov 1;18(21):6177-88. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10545127 10545127]
__TOC__
[[Category: DNA topoisomerase (ATP-hydrolyzing)]]
</StructureSection>
[[Category: Large Structures]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Single protein]]
[[Category: Berger JM]]
[[Category: Berger, J.M.]]
[[Category: DeAngelis KA]]
[[Category: DeAngelis, K.A.]]
[[Category: Keck JL]]
[[Category: Keck, J.L.]]
[[Category: Nichols MD]]
[[Category: Nichols, M.D.]]
[[Category: MG]]
[[Category: NA]]
[[Category: dna binding protein]]
[[Category: spo11 homolog]]
[[Category: topoisomerase vi]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 12:59:48 2007''

Latest revision as of 09:49, 7 February 2024

STRUCTURE OF THE DNA TOPOISOMERASE VI A SUBUNITSTRUCTURE OF THE DNA TOPOISOMERASE VI A SUBUNIT

Structural highlights

1d3y is a 2 chain structure with sequence from Methanocaldococcus jannaschii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TOP6A_METJA Relaxes both positive and negative superturns and exhibits a strong decatenase activity.[1]

Evolutionary Conservation

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

See Also

References

  1. ↑ Nichols MD, DeAngelis K, Keck JL, Berger JM. Structure and function of an archaeal topoisomerase VI subunit with homology to the meiotic recombination factor Spo11. EMBO J. 1999 Nov 1;18(21):6177-88. PMID:10545127 doi:10.1093/emboj/18.21.6177

1d3y, resolution 2.00Å

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