2au0: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
No edit summary
No edit summary
Line 1: Line 1:
[[Image:2au0.gif|left|200px]]<br /><applet load="2au0" size="350" color="white" frame="true" align="right" spinBox="true"
[[Image:2au0.gif|left|200px]]
caption="2au0, resolution 2.70&Aring;" />
 
'''Unmodified preinsertion binary complex'''<br />
{{Structure
|PDB= 2au0 |SIZE=350|CAPTION= <scene name='initialview01'>2au0</scene>, resolution 2.70&Aring;
|SITE=
|LIGAND= <scene name='pdbligand=CA:CALCIUM ION'>CA</scene>
|ACTIVITY= [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]
|GENE=
}}
 
'''Unmodified preinsertion binary complex'''
 


==Overview==
==Overview==
Line 7: Line 16:


==About this Structure==
==About this Structure==
2AU0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AU0 OCA].  
2AU0 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AU0 OCA].  


==Reference==
==Reference==
Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion., Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov NE, Patel DJ, PLoS Biol. 2006 Jan;4(1):e11. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16379496 16379496]
Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion., Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov NE, Patel DJ, PLoS Biol. 2006 Jan;4(1):e11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16379496 16379496]
[[Category: DNA-directed DNA polymerase]]
[[Category: DNA-directed DNA polymerase]]
[[Category: Single protein]]
[[Category: Single protein]]
Line 27: Line 36:
[[Category: y-family]]
[[Category: y-family]]


''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:30:58 2008''
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:53:49 2008''

Revision as of 16:53, 20 March 2008

File:2au0.gif


PDB ID 2au0

Drag the structure with the mouse to rotate
, resolution 2.70Å
Ligands:
Activity: DNA-directed DNA polymerase, with EC number 2.7.7.7
Coordinates: save as pdb, mmCIF, xml



Unmodified preinsertion binary complex


OverviewOverview

7,8-dihydro-8-oxoguanine (oxoG), the predominant lesion formed following oxidative damage of DNA by reactive oxygen species, is processed differently by replicative and bypass polymerases. Our kinetic primer extension studies demonstrate that the bypass polymerase Dpo4 preferentially inserts C opposite oxoG, and also preferentially extends from the oxoG*C base pair, thus achieving error-free bypass of this lesion. We have determined the crystal structures of preinsertion binary, insertion ternary, and postinsertion binary complexes of oxoG-modified template-primer DNA and Dpo4. These structures provide insights into the translocation mechanics of the bypass polymerase during a complete cycle of nucleotide incorporation. Specifically, during noncovalent dCTP insertion opposite oxoG (or G), the little-finger domain-DNA phosphate contacts translocate by one nucleotide step, while the thumb domain-DNA phosphate contacts remain fixed. By contrast, during the nucleotidyl transfer reaction that covalently incorporates C opposite oxoG, the thumb-domain-phosphate contacts are translocated by one nucleotide step, while the little-finger contacts with phosphate groups remain fixed. These stepwise conformational transitions accompanying nucleoside triphosphate binding and covalent nucleobase incorporation during a full replication cycle of Dpo4-catalyzed bypass of the oxoG lesion are distinct from the translocation events in replicative polymerases.

About this StructureAbout this Structure

2AU0 is a Single protein structure of sequence from Sulfolobus solfataricus. Full crystallographic information is available from OCA.

ReferenceReference

Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion., Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov NE, Patel DJ, PLoS Biol. 2006 Jan;4(1):e11. PMID:16379496

Page seeded by OCA on Thu Mar 20 15:53:49 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA