1s9f: Difference between revisions

Revision as of 15:59, 21 February 2008

DPO with AT matched

OverviewOverview

The ability or inability of a DNA polymerase to extend a mispair directly affects the establishment of genomic mutations. We report here kinetic analyses of the ability of Dpo4, a Y-family polymerase from Sulfolobus solfataricus, to extend from all mispairs opposite a template G or T. Dpo4 is equally inefficient at extending these mispairs, which include, surprisingly, a G.T mispair expected to conform closely to Watson-Crick geometry. To elucidate the basis of this, we solved the structure of Dpo4 bound to G.T-mispaired primer template in the presence of an incoming nucleotide. As a control, we also determined the structure of Dpo4 bound to a matched A-T base pair at the primer terminus. The structures offer a basis for the low efficiency of Dpo4 in extending a G.T mispair: a reverse wobble that deflects the primer 3'-OH away from the incoming nucleotide.

About this StructureAbout this Structure

1S9F is a Single protein structure of sequence from Sulfolobus solfataricus with , and as ligands. Active as DNA-directed DNA polymerase, with EC number 2.7.7.7 Full crystallographic information is available from OCA.

ReferenceReference

Dpo4 is hindered in extending a G.T mismatch by a reverse wobble., Trincao J, Johnson RE, Wolfle WT, Escalante CR, Prakash S, Prakash L, Aggarwal AK, Nat Struct Mol Biol. 2004 May;11(5):457-62. Epub 2004 Apr 11. PMID:15077104

Page seeded by OCA on Thu Feb 21 14:59:14 2008

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OCA

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-[[Image:1s9f.gif|left|200px]]<br /><applet load="1s9f" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1s9f.gif|left|200px]]<br /><applet load="1s9f" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1s9f, resolution 2.00&Aring;" />
 '''DPO with AT matched'''<br />
 ==Overview==
-The ability or inability of a DNA polymerase to extend a mispair directly, affects the establishment of genomic mutations. We report here kinetic, analyses of the ability of Dpo4, a Y-family polymerase from Sulfolobus, solfataricus, to extend from all mispairs opposite a template G or T. Dpo4, is equally inefficient at extending these mispairs, which include, surprisingly, a G.T mispair expected to conform closely to Watson-Crick, geometry. To elucidate the basis of this, we solved the structure of Dpo4, bound to G.T-mispaired primer template in the presence of an incoming, nucleotide. As a control, we also determined the structure of Dpo4 bound, to a matched A-T base pair at the primer terminus. The structures offer a, basis for the low efficiency of Dpo4 in extending a G.T mispair: a reverse, wobble that deflects the primer 3'-OH away from the incoming nucleotide.
+The ability or inability of a DNA polymerase to extend a mispair directly affects the establishment of genomic mutations. We report here kinetic analyses of the ability of Dpo4, a Y-family polymerase from Sulfolobus solfataricus, to extend from all mispairs opposite a template G or T. Dpo4 is equally inefficient at extending these mispairs, which include, surprisingly, a G.T mispair expected to conform closely to Watson-Crick geometry. To elucidate the basis of this, we solved the structure of Dpo4 bound to G.T-mispaired primer template in the presence of an incoming nucleotide. As a control, we also determined the structure of Dpo4 bound to a matched A-T base pair at the primer terminus. The structures offer a basis for the low efficiency of Dpo4 in extending a G.T mispair: a reverse wobble that deflects the primer 3'-OH away from the incoming nucleotide.
 ==About this Structure==
-S9F 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 CA, MG and DDY 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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1S9F OCA].
+S9F 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>, <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=DDY:'>DDY</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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S9F OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Single protein]]
 [[Category: Sulfolobus solfataricus]]
-[[Category: Aggarwal, A.K.]]
+[[Category: Aggarwal, A K.]]
-[[Category: Escalante, C.R.]]
+[[Category: Escalante, C R.]]
-[[Category: Johnson, R.E.]]
+[[Category: Johnson, R E.]]
 [[Category: Prakash, L.]]
 [[Category: Prakash, S.]]
 [[Category: Trincao, J.]]
-[[Category: Wolfle, W.T.]]
+[[Category: Wolfle, W T.]]
 [[Category: CA]]
 [[Category: DDY]]
@@ Line 26: / Line 26: @@
 [[Category: protein-dna complex]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 02:12:55 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:59:14 2008''