3bdp: Difference between revisions
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|PDB= 3bdp |SIZE=350|CAPTION= <scene name='initialview01'>3bdp</scene>, resolution 1.90Å | |PDB= 3bdp |SIZE=350|CAPTION= <scene name='initialview01'>3bdp</scene>, resolution 1.90Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=SO4:SULFATE ION'>SO4</scene> | |LIGAND= <scene name='pdbligand=2DT:3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE'>2DT</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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] | |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> | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|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> | |||
}} | }} | ||
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[[Category: Kiefer, J R.]] | [[Category: Kiefer, J R.]] | ||
[[Category: Mao, C.]] | [[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)]] | [[Category: complex (nucleotidyltransferase/dna)]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:25:21 2008'' | ||
Revision as of 05:25, 31 March 2008
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| , resolution 1.90Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Activity: | DNA-directed DNA polymerase, with EC number 2.7.7.7 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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
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