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| | <StructureSection load='1xwl' size='340' side='right'caption='[[1xwl]], [[Resolution|resolution]] 1.70Å' scene=''> | | <StructureSection load='1xwl' size='340' side='right'caption='[[1xwl]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1xwl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1bdp 1bdp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XWL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1XWL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1xwl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1bdp 1bdp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XWL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XWL FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BACILLUS STEAROTHERMOPHILUS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xwl OCA], [https://pdbe.org/1xwl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xwl RCSB], [https://www.ebi.ac.uk/pdbsum/1xwl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xwl ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1xwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xwl OCA], [http://pdbe.org/1xwl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xwl RCSB], [http://www.ebi.ac.uk/pdbsum/1xwl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xwl ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DPO1_GEOSE DPO1_GEOSE]] In addition to polymerase activity, this DNA polymerase exhibits 5' to 3' exonuclease activity. | + | [https://www.uniprot.org/uniprot/DPO1_GEOSE DPO1_GEOSE] In addition to polymerase activity, this DNA polymerase exhibits 5' to 3' exonuclease activity. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </div> | | </div> |
| | <div class="pdbe-citations 1xwl" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 1xwl" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 12980]] | + | [[Category: Geobacillus stearothermophilus]] |
| - | [[Category: DNA-directed DNA polymerase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Beese, L S]] | + | [[Category: Beese LS]] |
| - | [[Category: Kiefer, J R]] | + | [[Category: Kiefer JR]] |
| - | [[Category: Mao, C]] | + | [[Category: Mao C]] |
| - | [[Category: Bacillus stearothermophilus dna polymerase]]
| + | |
| - | [[Category: Bf thermophilus polymerase]]
| + | |
| - | [[Category: Dna replication]]
| + | |
| Structural highlights
Function
DPO1_GEOSE In addition to polymerase activity, this DNA polymerase exhibits 5' to 3' exonuclease activity.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
BACKGROUND: The study of DNA polymerases in the Pol l family is central to the understanding of DNA replication and repair. DNA polymerases are used in many molecular biology techniques, including PCR, which require a thermostable polymerase. In order to learn about Pol I function and the basis of thermostability, we undertook structural studies of a new thermostable DNA polymerase. RESULTS: A DNA polymerase large, Klenow-like, fragment from a recently identified thermostable strain of Bacillus stearothermophilus (BF) was cloned, sequenced, overexpressed and characterized. Its crystal structure was determined to 2.1 A resolution by the method of multiple isomorphous replacement. CONCLUSIONS: This structure represents the highest resolution view of a Pol I enzyme obtained to date. Comparison of the three Pol I structures reveals no compelling evidence for many of the specific interactions that have been proposed to induce thermostability, but suggests that thermostability arises from innumerable small changes distributed throughout the protein structure. The polymerase domain is highly conserved in all three proteins. The N-terminal domains are highly divergent in sequence, but retain a common fold. When present, the 3'-5' proofreading exonuclease activity is associated with this domain. Its absence is associated with changes in catalytic residues that coordinate the divalent ions required for activity and in loops connecting homologous secondary structural elements. In BF, these changes result in a blockage of the DNA-binding cleft.
Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution.,Kiefer JR, Mao C, Hansen CJ, Basehore SL, Hogrefe HH, Braman JC, Beese LS Structure. 1997 Jan 15;5(1):95-108. PMID:9016716[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kiefer JR, Mao C, Hansen CJ, Basehore SL, Hogrefe HH, Braman JC, Beese LS. Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution. Structure. 1997 Jan 15;5(1):95-108. PMID:9016716
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