1tgo: Difference between revisions

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-[[Image:1tgo.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1tgo", creates the "Structure Box" on the page.
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-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_1tgo|  PDB=1tgo  |  SCENE=  }}
-'''THERMOSTABLE B TYPE DNA POLYMERASE FROM THERMOCOCCUS GORGONARIUS'''
+==THERMOSTABLE B TYPE DNA POLYMERASE FROM THERMOCOCCUS GORGONARIUS==
+<StructureSection load='1tgo' size='340' side='right'caption='[[1tgo]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1tgo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_gorgonarius Thermococcus gorgonarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TGO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TGO 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]] 2.5&#8491;</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=1tgo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tgo OCA], [https://pdbe.org/1tgo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tgo RCSB], [https://www.ebi.ac.uk/pdbsum/1tgo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tgo ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPOL_THEGO DPOL_THEGO] In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity.
+== 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/tg/1tgo_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1tgo ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Most known archaeal DNA polymerases belong to the type B family, which also includes the DNA replication polymerases of eukaryotes, but maintain high fidelity at extreme conditions. We describe here the 2.5 A resolution crystal structure of a DNA polymerase from the Archaea Thermococcus gorgonarius and identify structural features of the fold and the active site that are likely responsible for its thermostable function. Comparison with the mesophilic B type DNA polymerase gp43 of the bacteriophage RB69 highlights thermophilic adaptations, which include the presence of two disulfide bonds and an enhanced electrostatic complementarity at the DNA-protein interface. In contrast to gp43, several loops in the exonuclease and thumb domains are more closely packed; this apparently blocks primer binding to the exonuclease active site. A physiological role of this "closed" conformation is unknown but may represent a polymerase mode, in contrast to an editing mode with an open exonuclease site. This archaeal B DNA polymerase structure provides a starting point for structure-based design of polymerases or ligands with applications in biotechnology and the development of antiviral or anticancer agents.
-==Overview==
+Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius.,Hopfner KP, Eichinger A, Engh RA, Laue F, Ankenbauer W, Huber R, Angerer B Proc Natl Acad Sci U S A. 1999 Mar 30;96(7):3600-5. PMID:10097083<ref>PMID:10097083</ref>
-Most known archaeal DNA polymerases belong to the type B family, which also includes the DNA replication polymerases of eukaryotes, but maintain high fidelity at extreme conditions. We describe here the 2.5 A resolution crystal structure of a DNA polymerase from the Archaea Thermococcus gorgonarius and identify structural features of the fold and the active site that are likely responsible for its thermostable function. Comparison with the mesophilic B type DNA polymerase gp43 of the bacteriophage RB69 highlights thermophilic adaptations, which include the presence of two disulfide bonds and an enhanced electrostatic complementarity at the DNA-protein interface. In contrast to gp43, several loops in the exonuclease and thumb domains are more closely packed; this apparently blocks primer binding to the exonuclease active site. A physiological role of this "closed" conformation is unknown but may represent a polymerase mode, in contrast to an editing mode with an open exonuclease site. This archaeal B DNA polymerase structure provides a starting point for structure-based design of polymerases or ligands with applications in biotechnology and the development of antiviral or anticancer agents.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-TGO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermococcus_gorgonarius Thermococcus gorgonarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TGO OCA].
+</div>
+<div class="pdbe-citations 1tgo" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius., Hopfner KP, Eichinger A, Engh RA, Laue F, Ankenbauer W, Huber R, Angerer B, Proc Natl Acad Sci U S A. 1999 Mar 30;96(7):3600-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10097083 10097083]
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-[[Category: DNA-directed DNA polymerase]]
+== References ==
-[[Category: Single protein]]
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Thermococcus gorgonarius]]
-[[Category: Angerer, B.]]
+[[Category: Angerer B]]
-[[Category: Ankenbauer, W.]]
+[[Category: Ankenbauer W]]
-[[Category: Eichinger, A.]]
+[[Category: Eichinger A]]
-[[Category: Engh, R A.]]
+[[Category: Engh RA]]
-[[Category: Hopfner, K P.]]
+[[Category: Hopfner K-P]]
-[[Category: Huber, R.]]
+[[Category: Huber R]]
-[[Category: Laue, F.]]
+[[Category: Laue F]]
-[[Category: Disulfide bond]]
-[[Category: Dna polymerase]]
-[[Category: Replication]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 09:55:47 2008''