2avt: Difference between revisions

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New page: left|200px<br /><applet load="2avt" size="350" color="white" frame="true" align="right" spinBox="true" caption="2avt, resolution 2.0Å" /> '''Crystal structure of ...
 
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[[Image:2avt.gif|left|200px]]<br /><applet load="2avt" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2avt, resolution 2.0&Aring;" />
'''Crystal structure of the beta subunit from DNA polymerase of Streptococcus pyogenes'''<br />


==Overview==
==Crystal structure of the beta subunit from DNA polymerase of Streptococcus pyogenes==
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.
<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/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='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]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/av/2avt_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=2avt ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2AVT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://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].
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16403212 16403212]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Streptococcus pyogenes]]
[[Category: Streptococcus pyogenes]]
[[Category: Argiriadi, M.A.]]
[[Category: Argiriadi MA]]
[[Category: Bruck, I.]]
[[Category: Bruck I]]
[[Category: Goedken, E.R.]]
[[Category: Goedken ER]]
[[Category: Kuriyan, J.]]
[[Category: Kuriyan J]]
[[Category: donnell, M.O.]]
[[Category: O'donnell M]]
[[Category: beta clamp]]
[[Category: polymerase]]
[[Category: replication]]
[[Category: sliding clamp]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 18:10:57 2008''

Latest revision as of 12:14, 14 February 2024

Crystal structure of the beta subunit from DNA polymerase of Streptococcus pyogenesCrystal structure of the beta subunit from DNA polymerase of Streptococcus pyogenes

Structural highlights

2avt is a 2 chain structure with sequence from Streptococcus pyogenes. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2avt, resolution 2.00Å

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