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1qss

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(New page: 200px<br /><applet load="1qss" size="450" color="white" frame="true" align="right" spinBox="true" caption="1qss, resolution 2.30&Aring;" /> '''DDGTP-TRAPPED CLOSED...)
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[[Image:1qss.gif|left|200px]]<br /><applet load="1qss" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1qss, resolution 2.30&Aring;" />
 
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'''DDGTP-TRAPPED CLOSED TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS'''<br />
 
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==Overview==
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==DDGTP-TRAPPED CLOSED TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS==
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The Taq DNA polymerase is the most commonly used enzyme in DNA sequencing., However, all versions of Taq polymerase are deficient in two respects: (i), these enzymes incorporate each of the four dideoxynucleoside 5', triphosphates (ddNTPs) at widely different rates during sequencing (ddGTP, for example, is incorporated 10 times faster than the other three ddNTPs), and (ii) these enzymes show uneven band-intensity or peak-height patterns, in radio-labeled or dye-labeled DNA sequence profiles, respectively. We, have determined the crystal structures of all four ddNTP-trapped closed, ternary complexes of the large fragment of the Taq DNA polymerase, (Klentaq1). The ddGTP-trapped complex structure differs from the other, three ternary complex structures by a large shift in the position of the, side chain of residue 660 in the O helix, resulting in additional hydrogen, bonds being formed between the guanidinium group of this residue and the, base of ddGTP. When Arg-660 is mutated to Asp, Ser, Phe, Tyr, or Leu, the, enzyme has a marked and selective reduction in ddGTP incorporation rate., As a result, the G track generated during DNA sequencing by these Taq, polymerase variants does not terminate prematurely, and higher, molecular-mass G bands are detected. Another property of these Taq, polymerase variants is that the sequencing patterns produced by these, enzymes are remarkably even in band-intensity and peak-height, distribution, thus resulting in a significant improvement in the accuracy, of DNA sequencing.
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<StructureSection load='1qss' size='340' side='right'caption='[[1qss]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1qss]] 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=1QSS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QSS FirstGlance]. <br>
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</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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene>, <scene name='pdbligand=DG3:2-3-DIDEOXYGUANOSINE-5-TRIPHOSPHATE'>DG3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qss OCA], [https://pdbe.org/1qss PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qss RCSB], [https://www.ebi.ac.uk/pdbsum/1qss PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qss ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DPO1_THEAQ DPO1_THEAQ]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qs/1qss_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1qss ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1QSS 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 DG3 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=1QSS OCA].
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation., Li Y, Mitaxov V, Waksman G, Proc Natl Acad Sci U S A. 1999 Aug 17;96(17):9491-6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10449720 10449720]
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[[Category: Large Structures]]
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[[Category: DNA-directed DNA polymerase]]
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[[Category: Single protein]]
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[[Category: Thermus aquaticus]]
[[Category: Thermus aquaticus]]
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[[Category: Li, Y.]]
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[[Category: Li Y]]
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[[Category: Mitaxov, V.]]
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[[Category: Mitaxov V]]
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[[Category: Waksman, G.]]
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[[Category: Waksman G]]
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[[Category: DG3]]
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[[Category: MG]]
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[[Category: closed]]
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[[Category: polymerase/dna]]
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[[Category: protein-dna complex]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:57:09 2007''
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Current revision

DDGTP-TRAPPED CLOSED TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS

PDB ID 1qss

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