2j6s: Difference between revisions

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[[Image:2j6s.gif|left|200px]]
[[Image:2j6s.gif|left|200px]]


{{Structure
<!--
|PDB= 2j6s |SIZE=350|CAPTION= <scene name='initialview01'>2j6s</scene>, resolution 2.50&Aring;
The line below this paragraph, containing "STRUCTURE_2j6s", creates the "Structure Box" on the page.
|SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Chain+A'>AC1</scene>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
|LIGAND= <scene name='pdbligand=6OG:6-O-METHYL+GUANOSINE-5&#39;-MONOPHOSPHATE'>6OG</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=DTP:2&#39;-DEOXYADENOSINE+5&#39;-TRIPHOSPHATE'>DTP</scene>
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
|ACTIVITY= <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>
or leave the SCENE parameter empty for the default display.
|GENE=  
-->
|DOMAIN=
{{STRUCTURE_2j6s| PDB=2j6s  | SCENE= }}  
|RELATEDENTRY=
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2j6s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j6s OCA], [http://www.ebi.ac.uk/pdbsum/2j6s PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2j6s RCSB]</span>
}}


'''TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-METHYLGUANINE MODIFIED DNA, AND DATP.'''
'''TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-METHYLGUANINE MODIFIED DNA, AND DATP.'''
Line 30: Line 27:
[[Category: Guengerich, F P.]]
[[Category: Guengerich, F P.]]
[[Category: Irimia, A.]]
[[Category: Irimia, A.]]
[[Category: dna damage]]
[[Category: Dna damage]]
[[Category: dna polymerase]]
[[Category: Dna polymerase]]
[[Category: dna repair]]
[[Category: Dna repair]]
[[Category: dna replication]]
[[Category: Dna replication]]
[[Category: dna-binding]]
[[Category: Dna-binding]]
[[Category: dna-directed dna polymerase]]
[[Category: Dna-directed dna polymerase]]
[[Category: dpo4]]
[[Category: Dpo4]]
[[Category: magnesium]]
[[Category: Magnesium]]
[[Category: metal-binding]]
[[Category: Metal-binding]]
[[Category: mutator protein]]
[[Category: Mutator protein]]
[[Category: nucleotidyltransferase]]
[[Category: Nucleotidyltransferase]]
[[Category: o6-methylguanine]]
[[Category: O6-methylguanine]]
[[Category: sulfolobus solfataricus]]
[[Category: Sulfolobus solfataricus]]
[[Category: transferase]]
[[Category: Transferase]]
[[Category: transferase/dna complex]]
[[Category: Transferase/dna complex]]
[[Category: translesion dna synthesis]]
[[Category: Translesion dna synthesis]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 08:25:43 2008''
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:53:47 2008''

Revision as of 05:25, 4 May 2008

File:2j6s.gif

Template:STRUCTURE 2j6s

TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6-METHYLGUANINE MODIFIED DNA, AND DATP.


Overview

We examined the effect of a single O6-methylguanine (O6-MeG) template residue on catalysis by a model Y family polymerase, Dpo4 from Sulfolobus solfataricus. Mass spectral analysis of Dpo4-catalyzed extension products revealed that the enzyme accurately bypasses O6-MeG, with C being the major product (approximately 70%) and T or A being the minor species (approximately 20% or approximately 10%, respectively), consistent with steady-state kinetic parameters. Transient-state kinetic experiments revealed that kpol, the maximum forward rate constant describing polymerization, for dCTP incorporation opposite O6-MeG was approximately 6-fold slower than observed for unmodified G, and no measurable product was observed for dTTP incorporation in the pre-steady state. The lack of any structural information regarding how O6-MeG paired in a polymerase active site led us to perform x-ray crystallographic studies, which show that "wobble" pairing occurs between C and O6-MeG. A structure containing T opposite O6-MeG was solved, but much of the ribose and pyrimidine base density was disordered, in accordance with a much higher Km,dTTP that drives the difference in efficiency between C and T incorporation. The more stabilized C:O6-MeG pairing reinforces the importance of hydrogen bonding with respect to nucleotide selection within a geometrically tolerant polymerase active site.

About this Structure

2J6S is a Single protein structure of sequence from Sulfolobus solfataricus. Full crystallographic information is available from OCA.

Reference

Sulfolobus solfataricus DNA polymerase Dpo4 is partially inhibited by "wobble" pairing between O6-methylguanine and cytosine, but accurate bypass is preferred., Eoff RL, Irimia A, Egli M, Guengerich FP, J Biol Chem. 2007 Jan 12;282(2):1456-67. Epub 2006 Nov 14. PMID:17105728 Page seeded by OCA on Sun May 4 08:25:43 2008

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