1d3y: Difference between revisions

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<StructureSection load='1d3y' size='340' side='right'caption='[[1d3y]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='1d3y' size='340' side='right'caption='[[1d3y]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1d3y]] is a 2 chain structure. 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>
<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='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>
</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA_topoisomerase_(ATP-hydrolyzing) DNA topoisomerase (ATP-hydrolyzing)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.99.1.3 5.99.1.3] </span></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>
<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>
</table>
== Function ==
== 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>
[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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].
</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>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:10545127<ref>PMID:10545127</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1d3y" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Berger, J M]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: DeAngelis, K A]]
[[Category: Berger JM]]
[[Category: Keck, J L]]
[[Category: DeAngelis KA]]
[[Category: Nichols, M D]]
[[Category: Keck JL]]
[[Category: Dna binding protein]]
[[Category: Nichols MD]]
[[Category: Isomerase]]
[[Category: Spo11 homolog]]
[[Category: Topoisomerase vi]]

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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