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| | ==Structure of E. coli Pol III 3mPHP mutant== | | ==Structure of E. coli Pol III 3mPHP mutant== |
| - | <StructureSection load='4jom' size='340' side='right' caption='[[4jom]], [[Resolution|resolution]] 2.90Å' scene=''> | + | <StructureSection load='4jom' size='340' side='right'caption='[[4jom]], [[Resolution|resolution]] 2.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4jom]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JOM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JOM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4jom]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JOM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JOM FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2hnh|2hnh]]</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=4jom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jom OCA], [https://pdbe.org/4jom PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jom RCSB], [https://www.ebi.ac.uk/pdbsum/4jom PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jom ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dnaE, polC, b0184, JW0179 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4jom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jom OCA], [http://pdbe.org/4jom PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jom RCSB], [http://www.ebi.ac.uk/pdbsum/4jom PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jom ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DPO3A_ECOLI DPO3A_ECOLI]] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The alpha chain is the DNA polymerase. | + | [https://www.uniprot.org/uniprot/DPO3A_ECOLI DPO3A_ECOLI] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The alpha chain is the DNA polymerase. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4jom" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4jom" style="background-color:#fffaf0;"></div> |
| - | | |
| - | ==See Also== | |
| - | *[[DNA polymerase|DNA polymerase]] | |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: DNA-directed DNA polymerase]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Ecoli]] | + | [[Category: Large Structures]] |
| - | [[Category: Anaya, J]] | + | [[Category: Anaya J]] |
| - | [[Category: Barros, T]] | + | [[Category: Barros T]] |
| - | [[Category: Donnell, M O]]
| + | [[Category: Guenther J]] |
| - | [[Category: Guenther, J]] | + | [[Category: Kelch B]] |
| - | [[Category: Kelch, B]] | + | [[Category: Kuriyan J]] |
| - | [[Category: Kuriyan, J]] | + | [[Category: Lamers MH]] |
| - | [[Category: Lamers, M H]] | + | [[Category: O'Donnell M]] |
| - | [[Category: Prabhakar, A]] | + | [[Category: Prabhakar A]] |
| - | [[Category: Dna binding]] | + | |
| - | [[Category: Dna polymerase]]
| + | |
| - | [[Category: Dntp binding]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
DPO3A_ECOLI DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The alpha chain is the DNA polymerase.
Publication Abstract from PubMed
BACKGROUND: In addition to the core catalytic machinery, bacterial replicative DNA polymerases contain a Polymerase and Histidinol Phosphatase (PHP) domain whose function is not entirely understood. The PHP domains of some bacterial replicases are active metal-dependent nucleases that may play a role in proofreading. In E. coli DNA polymerase III, however, the PHP domain has lost several metal-coordinating residues and is likely to be catalytically inactive. RESULTS: Genomic searches show that the loss of metal-coordinating residues in polymerase PHP domains is likely to have coevolved with the presence of a separate proofreading exonuclease that works with the polymerase. Although the E. coli Pol III PHP domain has lost metal-coordinating residues, the structure of the domain has been conserved to a remarkable degree when compared to that of metal-binding PHP domains. This is demonstrated by our ability to restore metal binding with only three point mutations, as confirmed by the metal-bound crystal structure of this mutant determined at 2.9 A resolution. We also show that Pol III, a large multi-domain protein, unfolds cooperatively and that mutations in the degenerate metal-binding site of the PHP domain decrease the overall stability of Pol III and reduce its activity. CONCLUSIONS: While the presence of a PHP domain in replicative bacterial polymerases is strictly conserved, its ability to coordinate metals and to perform proofreading exonuclease activity is not, suggesting additional non-enzymatic roles for the domain. Our results show that the PHP domain is a major structural element in Pol III and its integrity modulates both the stability and activity of the polymerase.
A structural role for the PHP domain in E. coli DNA polymerase III.,Barros T, Guenther J, Kelch B, Anaya J, Prabhakar A, O'Donnell M, Kuriyan J, Lamers MH BMC Struct Biol. 2013 May 14;13:8. doi: 10.1186/1472-6807-13-8. PMID:23672456[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Barros T, Guenther J, Kelch B, Anaya J, Prabhakar A, O'Donnell M, Kuriyan J, Lamers MH. A structural role for the PHP domain in E. coli DNA polymerase III. BMC Struct Biol. 2013 May 14;13:8. doi: 10.1186/1472-6807-13-8. PMID:23672456 doi:10.1186/1472-6807-13-8
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