1skr: Difference between revisions

Revision as of 08:49, 3 May 2008

T7 DNA Polymerase Complexed To DNA Primer/Template and ddATP

OverviewOverview

Ultraviolet-induced DNA damage poses a lethal block to replication. To understand the structural basis for this, we determined crystal structures of a replicative DNA polymerase from bacteriophage T7 in complex with nucleotide substrates and a DNA template containing a cis-syn cyclobutane pyrimidine dimer (CPD). When the 3' thymine is the templating base, the CPD is rotated out of the polymerase active site and the fingers subdomain adopts an open orientation. When the 5' thymine is the templating base, the CPD lies within the polymerase active site where it base-pairs with the incoming nucleotide and the 3' base of the primer, while the fingers are in a closed conformation. These structures reveal the basis for the strong block of DNA replication that is caused by this photolesion.

About this StructureAbout this Structure

1SKR is a Protein complex structure of sequences from Enterobacteria phage t7 and Escherichia coli. Full crystallographic information is available from OCA.

ReferenceReference

Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7., Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS, Ellenberger T, Nat Struct Mol Biol. 2004 Aug;11(8):784-90. Epub 2004 Jul 4. PMID:15235589 Page seeded by OCA on Sat May 3 08:49:24 2008

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

OCA

@@ Line 1: / Line 1: @@
 [[Image:1skr.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 1skr |SIZE=350|CAPTION= <scene name='initialview01'>1skr</scene>, resolution 2.4&Aring;
+The line below this paragraph, containing "STRUCTURE_1skr", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=2DA:2&#39;,3&#39;-DIDEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>2DA</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DAD:2&#39;,3&#39;-DIDEOXYADENOSINE-5&#39;-TRIPHOSPHATE'>DAD</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=MG:MAGNESIUM+ION'>MG</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= 5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10760 Enterobacteria phage T7]), TRXA, TSNC, FIPA, B3781, C4701, Z5291, ECS4714, STM3915, STMD1.75, STY3639, T3381, SF3854, S3905 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+-->
-|DOMAIN=
+{{STRUCTURE_1skr|  PDB=1skr  |  SCENE=  }}
-|RELATEDENTRY=[[1t7p|1T7P]], [[1sks|1SKS]], [[1skw|1SKW]], [[1sl0|1SL0]], [[1sl1|1SL1]], [[1sl2|1SL2]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1skr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1skr OCA], [http://www.ebi.ac.uk/pdbsum/1skr PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1skr RCSB]</span>
-}}
 '''T7 DNA Polymerase Complexed To DNA Primer/Template and ddATP'''
@@ Line 33: / Line 30: @@
 [[Category: Li, Y.]]
 [[Category: Taylor, J S.]]
-[[Category: close]]
+[[Category: Close]]
-[[Category: dna polymerase]]
+[[Category: Dna polymerase]]
-[[Category: open]]
+[[Category: Open]]
-[[Category: replication]]
+[[Category: Replication]]
-[[Category: uv-lesion]]
+[[Category: Uv-lesion]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 08:49:24 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:43:21 2008''