2avt: Difference between revisions

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 <StructureSection load='2avt' size='340' side='right'caption='[[2avt]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2avt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_scarlatinae"_klein_1884 "micrococcus scarlatinae" klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AVT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AVT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2avt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pyogenes Streptococcus pyogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AVT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AVT FirstGlance]. <br>
-</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=2avt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2avt OCA], [https://pdbe.org/2avt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2avt RCSB], [https://www.ebi.ac.uk/pdbsum/2avt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2avt ProSAT]</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&#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=2avt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2avt OCA], [https://pdbe.org/2avt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2avt RCSB], [https://www.ebi.ac.uk/pdbsum/2avt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2avt ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9EVR1_STRPY Q9EVR1_STRPY] Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP-independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of replication as well as for processivity of DNA replication.[ARBA:ARBA00002266]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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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=2avt ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-BACKGROUND: Sliding DNA clamps are processivity factors that are required for efficient DNA replication. DNA polymerases maintain proximity to nucleic acid templates by interacting with sliding clamps that encircle DNA and thereby link the polymerase enzyme to the DNA substrate. Although the structures of sliding clamps from Gram-negative bacteria (E. coli), eukaryotes, archaea, and T4-like bacteriophages are well-known, the structure of a sliding clamp from Gram-positive bacteria has not been reported previously. RESULTS: We have determined the crystal structure of the dimeric beta subunit of the DNA polymerase III holoenzyme of Streptococcus pyogenes. The sliding clamp from this Gram-positive organism forms a ring-shaped dimeric assembly that is similar in overall structure to that of the sliding clamps from Gram-negative bacteria, bacteriophage T4, eukaryotes and archaea. The dimer has overall dimensions of approximately 90 A x approximately 70 A x approximately 25 A with a central chamber that is large enough to accommodate duplex DNA. In comparison to the circular shape of other assemblies, the S. pyogenes clamp adopts a more elliptical structure. CONCLUSION: The sequences of sliding clamps from S. pyogenes and E. coli are only 23% identical, making the generation of structural models for the S. pyogenes clamp difficult in the absence of direct experimental information. Our structure of the S. pyogenes beta subunit completes the catalog of clamp structures from all the major sequence grouping of sliding clamps. The more elliptical rather than circular structure of the S. pyogenes clamp implies that the topological nature of encircling DNA, rather than a precise geometric shape, is the most conserved aspect for this family of proteins.
-Crystal structure of a DNA polymerase sliding clamp from a Gram-positive bacterium.,Argiriadi MA, Goedken ER, Bruck I, O'Donnell M, Kuriyan J BMC Struct Biol. 2006 Jan 10;6:2. PMID:16403212<ref>PMID:16403212</ref>
+==See Also==
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2avt" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Micrococcus scarlatinae klein 1884]]
 [[Category: Large Structures]]
-[[Category: Argiriadi, M A]]
+[[Category: Streptococcus pyogenes]]
-[[Category: Bruck, I]]
+[[Category: Argiriadi MA]]
-[[Category: Goedken, E R]]
+[[Category: Bruck I]]
-[[Category: Kuriyan, J]]
+[[Category: Goedken ER]]
-[[Category: Donnell, M O]]
+[[Category: Kuriyan J]]
-[[Category: Beta clamp]]
+[[Category: O'donnell M]]
-[[Category: Polymerase]]
-[[Category: Replication]]
-[[Category: Sliding clamp]]
-[[Category: Transferase]]