2ae9: Difference between revisions

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-[[Image:2ae9.gif|left|200px]]
- {{Structure
+==Solution Structure of the theta subunit of DNA polymerase III from E. coli==
-|PDB= 2ae9 |SIZE=350|CAPTION= <scene name='initialview01'>2ae9</scene>
+<StructureSection load='2ae9' size='340' side='right'caption='[[2ae9]]' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND=
+<table><tr><td colspan='2'>[[2ae9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AE9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AE9 FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[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] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-|GENE= holE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ae9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ae9 OCA], [https://pdbe.org/2ae9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ae9 RCSB], [https://www.ebi.ac.uk/pdbsum/2ae9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ae9 ProSAT]</span></td></tr>
-|DOMAIN=
+</table>
-|RELATEDENTRY=
+== Function ==
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ae9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ae9 OCA], [http://www.ebi.ac.uk/pdbsum/2ae9 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2ae9 RCSB]</span>
+[https://www.uniprot.org/uniprot/HOLE_ECOLI HOLE_ECOLI] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity.  The exact function of the theta subunit is unknown.
-}}
+== 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/ae/2ae9_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=2ae9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The catalytic core of Escherichia coli DNA polymerase III holoenzyme contains three subunits: alpha, epsilon, and theta. The alpha subunit contains the polymerase, and the epsilon subunit contains the exonucleolytic proofreading function. The small (8-kDa) theta subunit binds only to epsilon. Its function is not well understood, although it was shown to exert a small stabilizing effect on the epsilon proofreading function. In order to help elucidate its function, we undertook a determination of its solution structure. In aqueous solution, theta yielded poor-quality nuclear magnetic resonance spectra, presumably due to conformational exchange and/or protein aggregation. Based on our recently determined structure of the theta homolog from bacteriophage P1, named HOT, we constructed a homology model of theta. This model suggested that the unfavorable behavior of theta might arise from exposed hydrophobic residues, particularly toward the end of alpha-helix 3. In gel filtration studies, theta elutes later than expected, indicating that aggregation is potentially responsible for these problems. To address this issue, we recorded 1H-15N heteronuclear single quantum correlation (HSQC) spectra in water-alcohol mixed solvents and observed substantially improved dispersion and uniformity of peak intensities, facilitating a structural determination under these conditions. The structure of theta in 60/40 (vol/vol) water-methanol is similar to that of HOT but differs significantly from a previously reported theta structure. The new theta structure is expected to provide additional insight into its physiological role and its effect on the epsilon proofreading subunit.
-'''Solution Structure of the theta subunit of DNA polymerase III from E. coli'''
+Nuclear magnetic resonance solution structure of the Escherichia coli DNA polymerase III theta subunit.,Mueller GA, Kirby TW, DeRose EF, Li D, Schaaper RM, London RE J Bacteriol. 2005 Oct;187(20):7081-9. PMID:16199579<ref>PMID:16199579</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2ae9" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-The catalytic core of Escherichia coli DNA polymerase III holoenzyme contains three subunits: alpha, epsilon, and theta. The alpha subunit contains the polymerase, and the epsilon subunit contains the exonucleolytic proofreading function. The small (8-kDa) theta subunit binds only to epsilon. Its function is not well understood, although it was shown to exert a small stabilizing effect on the epsilon proofreading function. In order to help elucidate its function, we undertook a determination of its solution structure. In aqueous solution, theta yielded poor-quality nuclear magnetic resonance spectra, presumably due to conformational exchange and/or protein aggregation. Based on our recently determined structure of the theta homolog from bacteriophage P1, named HOT, we constructed a homology model of theta. This model suggested that the unfavorable behavior of theta might arise from exposed hydrophobic residues, particularly toward the end of alpha-helix 3. In gel filtration studies, theta elutes later than expected, indicating that aggregation is potentially responsible for these problems. To address this issue, we recorded 1H-15N heteronuclear single quantum correlation (HSQC) spectra in water-alcohol mixed solvents and observed substantially improved dispersion and uniformity of peak intensities, facilitating a structural determination under these conditions. The structure of theta in 60/40 (vol/vol) water-methanol is similar to that of HOT but differs significantly from a previously reported theta structure. The new theta structure is expected to provide additional insight into its physiological role and its effect on the epsilon proofreading subunit.
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-AE9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AE9 OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Nuclear magnetic resonance solution structure of the Escherichia coli DNA polymerase III theta subunit., Mueller GA, Kirby TW, DeRose EF, Li D, Schaaper RM, London RE, J Bacteriol. 2005 Oct;187(20):7081-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16199579 16199579]
-[[Category: DNA-directed DNA polymerase]]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Derose, E F.]]
+[[Category: Derose EF]]
-[[Category: Kirby, T W.]]
+[[Category: Kirby TW]]
-[[Category: Li, D.]]
+[[Category: Li D]]
-[[Category: London, R E.]]
+[[Category: London RE]]
-[[Category: Mueller, G A.]]
+[[Category: Mueller GA]]
-[[Category: Schaaper, R M.]]
+[[Category: Schaaper RM]]
-[[Category: 3 helice]]
-[[Category: all helical]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:51:25 2008''