3i2m: Difference between revisions
No edit summary |
No edit summary |
||
| (7 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
< | ==The Crystal Structure of PF-8, the DNA Polymerase Accessory Subunit from Kaposi s Sarcoma-Associated Herpesvirus== | ||
<StructureSection load='3i2m' size='340' side='right'caption='[[3i2m]], [[Resolution|resolution]] 2.81Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3i2m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_gammaherpesvirus_8 Human gammaherpesvirus 8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I2M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I2M 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]] 2.81Å</td></tr> | |||
-- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=3i2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i2m OCA], [https://pdbe.org/3i2m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i2m RCSB], [https://www.ebi.ac.uk/pdbsum/3i2m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i2m ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q77ZG5_HHV8 Q77ZG5_HHV8] | |||
== 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/i2/3i2m_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=3i2m ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Kaposi's sarcoma-associated herpesvirus is an emerging pathogen whose mechanism of replication is poorly understood. PF-8, the presumed processivity factor of Kaposi's sarcoma-associated herpesvirus DNA polymerase, acts in combination with the catalytic subunit, Pol-8, to synthesize viral DNA. We have solved the crystal structure of residues 1 to 304 of PF-8 at a resolution of 2.8 A. This structure reveals that each monomer of PF-8 shares a fold common to processivity factors. Like human cytomegalovirus UL44, PF-8 forms a head-to-head dimer in the form of a C clamp, with its concave face containing a number of basic residues that are predicted to be important for DNA binding. However, there are several differences with related proteins, especially in loops that extend from each monomer into the center of the C clamp and in the loops that connect the two subdomains of each protein, which may be important for determining PF-8's mode of binding to DNA and to Pol-8. Using the crystal structures of PF-8, the herpes simplex virus catalytic subunit, and RB69 bacteriophage DNA polymerase in complex with DNA and initial experiments testing the effects of inhibition of PF-8-stimulated DNA synthesis by peptides derived from Pol-8, we suggest a model for how PF-8 might form a ternary complex with Pol-8 and DNA. The structure and the model suggest interesting similarities and differences in how PF-8 functions relative to structurally similar proteins. | |||
The crystal structure of PF-8, the DNA polymerase accessory subunit from Kaposi's sarcoma-associated herpesvirus.,Baltz JL, Filman DJ, Ciustea M, Silverman JE, Lautenschlager CL, Coen DM, Ricciardi RP, Hogle JM J Virol. 2009 Dec;83(23):12215-28. Epub 2009 Sep 16. PMID:19759157<ref>PMID:19759157</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3i2m" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Human gammaherpesvirus 8]] | ||
[[Category: Large Structures]] | |||
[[Category: Baltz JL]] | |||
== | [[Category: Ciustea M]] | ||
< | [[Category: Coen DM]] | ||
[[Category: Human | [[Category: Filman DJ]] | ||
[[Category: Baltz | [[Category: Hogle JM]] | ||
[[Category: Ciustea | [[Category: Lautenschlager CL]] | ||
[[Category: Coen | [[Category: Ricciardi RP]] | ||
[[Category: Filman | [[Category: Silverman JEY]] | ||
[[Category: Hogle | |||
[[Category: Lautenschlager | |||
[[Category: Ricciardi | |||
[[Category: Silverman | |||
Latest revision as of 12:16, 30 October 2024
The Crystal Structure of PF-8, the DNA Polymerase Accessory Subunit from Kaposi s Sarcoma-Associated HerpesvirusThe Crystal Structure of PF-8, the DNA Polymerase Accessory Subunit from Kaposi s Sarcoma-Associated Herpesvirus
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedKaposi's sarcoma-associated herpesvirus is an emerging pathogen whose mechanism of replication is poorly understood. PF-8, the presumed processivity factor of Kaposi's sarcoma-associated herpesvirus DNA polymerase, acts in combination with the catalytic subunit, Pol-8, to synthesize viral DNA. We have solved the crystal structure of residues 1 to 304 of PF-8 at a resolution of 2.8 A. This structure reveals that each monomer of PF-8 shares a fold common to processivity factors. Like human cytomegalovirus UL44, PF-8 forms a head-to-head dimer in the form of a C clamp, with its concave face containing a number of basic residues that are predicted to be important for DNA binding. However, there are several differences with related proteins, especially in loops that extend from each monomer into the center of the C clamp and in the loops that connect the two subdomains of each protein, which may be important for determining PF-8's mode of binding to DNA and to Pol-8. Using the crystal structures of PF-8, the herpes simplex virus catalytic subunit, and RB69 bacteriophage DNA polymerase in complex with DNA and initial experiments testing the effects of inhibition of PF-8-stimulated DNA synthesis by peptides derived from Pol-8, we suggest a model for how PF-8 might form a ternary complex with Pol-8 and DNA. The structure and the model suggest interesting similarities and differences in how PF-8 functions relative to structurally similar proteins. The crystal structure of PF-8, the DNA polymerase accessory subunit from Kaposi's sarcoma-associated herpesvirus.,Baltz JL, Filman DJ, Ciustea M, Silverman JE, Lautenschlager CL, Coen DM, Ricciardi RP, Hogle JM J Virol. 2009 Dec;83(23):12215-28. Epub 2009 Sep 16. PMID:19759157[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
|
| ||||||||||||||||||