2uvu: Difference between revisions

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Revision as of 19:40, 20 March 2008

File:2uvu.jpg

, resolution 2.70Å

Sites:

Ligands:

and

Activity:

DNA-directed DNA polymerase, with EC number 2.7.7.7

Coordinates:

save as pdb, mmCIF, xml

CRYSTAL STRUCTURES OF MUTANT DPO4 DNA POLYMERASES WITH 8-OXOG CONTAINING DNA TEMPLATE-PRIMER CONSTRUCTS

OverviewOverview

Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) has been shown to catalyze bypass of 7,8-dihydro-8-oxodeoxyguanosine (8-oxoG) in a highly efficient and relatively accurate manner. Crystal structures have revealed a potential role for Arg(332) in stabilizing the anti conformation of the 8-oxoG template base by means of a hydrogen bond or ion-dipole pair, which results in an increased enzymatic efficiency for dCTP insertion and makes formation of a Hoogsteen pair between 8-oxoG and dATP less favorable. Site-directed mutagenesis was used to replace Arg(332) with Ala, Glu, Leu, or His in order to probe the importance of Arg(332) in accurate and efficient bypass of 8-oxoG. The double mutant Ala(331)Ala(332) was also prepared to address the contribution of Arg(331). Transientstate kinetic results suggest that Glu(332) retains fidelity against bypass of 8-oxoG that is similar to wild type Dpo4, a result that was confirmed by tandem mass spectrometric analysis of full-length extension products. A crystal structure of the Dpo4 Glu(332) mutant and 8-oxoG:C pair revealed water-mediated hydrogen bonds between Glu(332) and the O-8 atom of 8-oxoG. The space normally occupied by Arg(332) side chain is empty in the crystal structures of the Ala(332) mutant. Two other crystal structures show that a Hoogsteen base pair is formed between 8-oxoG and A in the active site of both Glu(332) and Ala(332) mutants. These results support the view that a bond between Arg(332) and 8-oxoG plays a role in determining the fidelity and efficiency of Dpo4-catalyzed bypass of the lesion.

About this StructureAbout this Structure

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

ReferenceReference

Hydrogen bonding of 7,8-dihydro-8-oxodeoxyguanosine with a charged residue in the little finger domain determines miscoding events in Sulfolobus solfataricus DNA polymerase Dpo4., Eoff RL, Irimia A, Angel KC, Egli M, Guengerich FP, J Biol Chem. 2007 Jul 6;282(27):19831-43. Epub 2007 Apr 27. PMID:17468100

Page seeded by OCA on Thu Mar 20 18:40:26 2008

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OCA

@@ Line 1: / Line 1: @@
-[[Image:2uvu.jpg|left|200px]]<br /><applet load="2uvu" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:2uvu.jpg|left|200px]]
-caption="2uvu, resolution 2.70&Aring;" />
-'''CRYSTAL STRUCTURES OF MUTANT DPO4 DNA POLYMERASES WITH 8-OXOG CONTAINING DNA TEMPLATE-PRIMER CONSTRUCTS'''<br />
+ {{Structure
+|PDB= 2uvu |SIZE=350|CAPTION= <scene name='initialview01'>2uvu</scene>, resolution 2.70&Aring;
+|SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Chain+A'>AC1</scene>
+|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=DGT:2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE'>DGT</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=
+}}
+'''CRYSTAL STRUCTURES OF MUTANT DPO4 DNA POLYMERASES WITH 8-OXOG CONTAINING DNA TEMPLATE-PRIMER CONSTRUCTS'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-UVU 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> and <scene name='pdbligand=DGT:'>DGT</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. 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] Known structural/functional Site: <scene name='pdbsite=AC1:Ca+Binding+Site+For+Chain+A'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2UVU OCA].
+UVU 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=2UVU OCA].
 ==Reference==
-Hydrogen bonding of 7,8-dihydro-8-oxodeoxyguanosine with a charged residue in the little finger domain determines miscoding events in Sulfolobus solfataricus DNA polymerase Dpo4., Eoff RL, Irimia A, Angel KC, Egli M, Guengerich FP, J Biol Chem. 2007 Jul 6;282(27):19831-43. Epub 2007 Apr 27. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17468100 17468100]
+Hydrogen bonding of 7,8-dihydro-8-oxodeoxyguanosine with a charged residue in the little finger domain determines miscoding events in Sulfolobus solfataricus DNA polymerase Dpo4., Eoff RL, Irimia A, Angel KC, Egli M, Guengerich FP, J Biol Chem. 2007 Jul 6;282(27):19831-43. Epub 2007 Apr 27. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17468100 17468100]
 [[Category: DNA-directed DNA polymerase]]
 [[Category: Single protein]]
@@ Line 35: / Line 44: @@
 [[Category: translesion dna polymerase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:50:44 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:40:26 2008''