1em8: Difference between revisions

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 ==Crystal structure of chi and psi subunit heterodimer from DNA POL III==
-<StructureSection load='1em8' size='340' side='right' caption='[[1em8]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='1em8' size='340' side='right'caption='[[1em8]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1em8]] is a 4 chain structure with 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=1EM8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EM8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1em8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EM8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EM8 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1em8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1em8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1em8 RCSB], [http://www.ebi.ac.uk/pdbsum/1em8 PDBsum]</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=1em8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1em8 OCA], [https://pdbe.org/1em8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1em8 RCSB], [https://www.ebi.ac.uk/pdbsum/1em8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1em8 ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HOLC_ECOLI HOLC_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.
 == 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/em/1em8_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/em/1em8_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/chain_selection.php?pdb_ID=2ata 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=1em8 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The chi (chi) and psi (psi) subunits of Escherichia coli DNA polymerase III form a heterodimer that is associated with the ATP-dependent clamp-loader machinery. In E. coli, the chi:psi heterodimer serves as a bridge between the clamp-loader complex and the single-stranded DNA-binding protein. We determined the crystal structure of the chi:psi heterodimer at 2.1 A resolution. Although neither chi (147 residues) nor psi (137 residues) bind to nucleotides, the fold of each protein is similar to the folds of mononucleotide-(chi) or dinucleotide-(psi) binding proteins, without marked similarity to the structures of the clamp-loader subunits. Genes encoding chi and psi proteins are found to be readily identifiable in several bacterial genomes and sequence alignments showed that residues at the chi:psi interface are highly conserved in both proteins, suggesting that the heterodimeric interaction is of functional significance. The conservation of surface-exposed residues is restricted to the interfacial region and to just two other regions in the chi:psi complex. One of the conserved regions was found to be located on chi, distal to the psi interaction region, and we identified this as the binding site for a C-terminal segment of the single-stranded DNA-binding protein. The other region of sequence conservation is localized to an N-terminal segment of psi (26 residues) that is disordered in the crystal structure. We speculate that psi is linked to the clamp-loader complex by this flexible, but conserved, N-terminal segment, and that the chi:psi unit is linked to the single-stranded DNA-binding protein via the distal surface of chi. The base of the clamp-loader complex has an open C-shaped structure, and the shape of the chi:psi complex is suggestive of a loose docking within the crevice formed by the open faces of the delta and delta' subunits of the clamp-loader.
-Crystal structure of the chi:psi sub-assembly of the Escherichia coli DNA polymerase clamp-loader complex.,Gulbis JM, Kazmirski SL, Finkelstein J, Kelman Z, O'Donnell M, Kuriyan J Eur J Biochem. 2004 Jan;271(2):439-49. PMID:14717711<ref>PMID:14717711</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[DNA polymerase|DNA polymerase]]
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: DNA-directed DNA polymerase]]
 [[Category: Escherichia coli]]
-[[Category: Donnell, M O.]]
+[[Category: Large Structures]]
-[[Category: Finkelstein, J.]]
+[[Category: Finkelstein J]]
-[[Category: Gulbis, J M.]]
+[[Category: Gulbis JM]]
-[[Category: Kuriyan, J.]]
+[[Category: Kuriyan J]]
-[[Category: Alpha-beta fold]]
+[[Category: O'Donnell M]]
-[[Category: Clamp-loader]]
-[[Category: Dna pol iii]]
-[[Category: Gene regulation]]
-[[Category: Heterodimer]]