2ktq: Difference between revisions

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New page: left|200px<br /><applet load="2ktq" size="450" color="white" frame="true" align="right" spinBox="true" caption="2ktq, resolution 2.3Å" /> '''OPEN TERNARY COMPLEX ...
 
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[[Image:2ktq.gif|left|200px]]<br /><applet load="2ktq" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2ktq, resolution 2.3&Aring;" />
'''OPEN TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS'''<br />


==Overview==
==OPEN TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS==
The crystal structures of two ternary complexes of the large fragment of, Thermus aquaticus DNA polymerase I (Klentaq1) with a primer/template DNA, and dideoxycytidine triphosphate, and that of a binary complex of the same, enzyme with a primer/template DNA, were determined to a resolution of 2.3, 2.3 and 2.5 A, respectively. One ternary complex structure differs, markedly from the two other structures by a large reorientation of the tip, of the fingers domain. This structure, designated 'closed', represents the, ternary polymerase complex caught in the act of incorporating a, nucleotide. In the two other structures, the tip of the fingers domain is, rotated outward by 46 degrees ('open') in an orientation similar to that, of the apo form of Klentaq1. These structures provide the first direct, evidence in DNA polymerase I enzymes of a large conformational change, responsible for assembling an active ternary complex.
<StructureSection load='2ktq' size='340' side='right'caption='[[2ktq]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2ktq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KTQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KTQ 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]] 2.3&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCT:2,3-DIDEOXYCYTIDINE+5-TRIPHOSPHATE'>DCT</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=2ktq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ktq OCA], [https://pdbe.org/2ktq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ktq RCSB], [https://www.ebi.ac.uk/pdbsum/2ktq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ktq ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DPO1_THEAQ DPO1_THEAQ]
== 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/kt/2ktq_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=2ktq ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2KTQ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus] with MG and DCT as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2KTQ OCA].
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation., Li Y, Korolev S, Waksman G, EMBO J. 1998 Dec 15;17(24):7514-25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9857206 9857206]
[[Category: Large Structures]]
[[Category: DNA-directed DNA polymerase]]
[[Category: Single protein]]
[[Category: Thermus aquaticus]]
[[Category: Thermus aquaticus]]
[[Category: Li, Y.]]
[[Category: Li Y]]
[[Category: Waksman, G.]]
[[Category: Waksman G]]
[[Category: DCT]]
[[Category: MG]]
[[Category: large fragement of taq dna polymerase i]]
[[Category: protein/dna]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 12:41:08 2007''

Latest revision as of 09:04, 21 February 2024

OPEN TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS

2ktq, resolution 2.30Å

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