3bdp: Difference between revisions

Revision as of 20:39, 4 May 2008

DNA POLYMERASE I/DNA COMPLEX

OverviewOverview

DNA polymerases copy DNA templates with remarkably high fidelity, checking for correct base-pair formation both at nucleotide insertion and at subsequent DNA extension steps. Despite extensive biochemical, genetic and structural studies, the mechanism by which nucleotides are correctly incorporated is not known. Here we present high-resolution crystal structures of a thermostable bacterial (Bacillus stearothermophilus) DNA polymerase I large fragments with DNA primer templates bound productively at the polymerase active site. The active site retains catalytic activity, allowing direct observation of the products of several rounds of nucleotide incorporation. The polymerase also retains its ability to discriminate between correct and incorrectly paired nucleotides in the crystal. Comparison of the structures of successively translocated complexes allows the structural features for the sequence-independent molecular recognition of correctly formed base pairs to be deduced unambiguously. These include extensive interactions with the first four to five base pairs in the minor groove, location of the terminal base pair in a pocket of excellent steric complementarity favouring correct base-pair formation, and a conformational switch from B-form to underwound A-form DNA at the polymerase active site.

About this StructureAbout this Structure

3BDP is a Single protein structure of sequence from Geobacillus stearothermophilus. Full crystallographic information is available from OCA.

ReferenceReference

Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal., Kiefer JR, Mao C, Braman JC, Beese LS, Nature. 1998 Jan 15;391(6664):304-7. PMID:9440698 Page seeded by OCA on Sun May 4 20:39:49 2008

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OCA

@@ Line 1: / Line 1: @@
 [[Image:3bdp.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 3bdp |SIZE=350|CAPTION= <scene name='initialview01'>3bdp</scene>, resolution 1.90&Aring;
+The line below this paragraph, containing "STRUCTURE_3bdp", 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=2DT:3&#39;-DEOXYTHYMIDINE-5&#39;-MONOPHOSPHATE'>2DT</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=SO4:SULFATE+ION'>SO4</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_3bdp|  PDB=3bdp  |  SCENE=  }}
-|RELATEDENTRY=
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bdp OCA], [http://www.ebi.ac.uk/pdbsum/3bdp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3bdp RCSB]</span>
-}}
 '''DNA POLYMERASE I/DNA COMPLEX'''
@@ Line 29: / Line 26: @@
 [[Category: Kiefer, J R.]]
 [[Category: Mao, C.]]
-[[Category: bacillus stearothermophilus dna polymerase]]
+[[Category: Bacillus stearothermophilus dna polymerase]]
-[[Category: bf thermophilus polymerase]]
+[[Category: Bf thermophilus polymerase]]
-[[Category: complex (nucleotidyltransferase/dna)]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 20:39:49 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:25:21 2008''