3f2b: Difference between revisions
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< | ==DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mg and Zn== | ||
<StructureSection load='3f2b' size='340' side='right'caption='[[3f2b]], [[Resolution|resolution]] 2.39Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3f2b]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F2B FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.39Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=3f2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f2b OCA], [https://pdbe.org/3f2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f2b RCSB], [https://www.ebi.ac.uk/pdbsum/3f2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f2b ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q5L0J3_GEOKA Q5L0J3_GEOKA] Required for replicative DNA synthesis. This DNA polymerase also exhibits 3' to 5' exonuclease activity (By similarity).[HAMAP-Rule:MF_00356][SAAS:SAAS029460_004_008054] | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f2/3f2b_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3f2b ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
PolC is the polymerase responsible for genome duplication in many Gram-positive bacteria and represents an attractive target for antibacterial development. We have determined the 2.4-A resolution crystal structure of Geobacillus kaustophilus PolC in a ternary complex with DNA and dGTP. The structure reveals nascent base pair interactions that lead to highly accurate nucleotide incorporation. A unique beta-strand motif in the PolC thumb domain contacts the minor groove, allowing replication errors to be sensed up to 8 nt upstream of the active site. PolC exhibits the potential for large-scale conformational flexibility, which could encompass the catalytic residues. The structure suggests a mechanism by which the active site can communicate with the rest of the replisome to trigger proofreading after nucleotide misincorporation, leading to an integrated model for controlling the dynamic switch between replicative and repair polymerases. This ternary complex of a cellular replicative polymerase affords insights into polymerase fidelity, evolution, and structural diversity. | |||
Structure of PolC reveals unique DNA binding and fidelity determinants.,Evans RJ, Davies DR, Bullard JM, Christensen J, Green LS, Guiles JW, Pata JD, Ribble WK, Janjic N, Jarvis TC Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):20695-700. Epub 2008 Dec 23. PMID:19106298<ref>PMID:19106298</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3f2b" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
== | |||
< | |||
[[Category: Geobacillus kaustophilus]] | [[Category: Geobacillus kaustophilus]] | ||
[[Category: Bullard | [[Category: Large Structures]] | ||
[[Category: Christensen | [[Category: Bullard JM]] | ||
[[Category: Davies | [[Category: Christensen J]] | ||
[[Category: Evans | [[Category: Davies DR]] | ||
[[Category: Green | [[Category: Evans RJ]] | ||
[[Category: Guiles | [[Category: Green LS]] | ||
[[Category: Janjic | [[Category: Guiles JW]] | ||
[[Category: Jarvis | [[Category: Janjic N]] | ||
[[Category: Ribble | [[Category: Jarvis TC]] | ||
[[Category: Ribble WK]] | |||
Latest revision as of 03:28, 28 December 2023
DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mg and ZnDNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mg and Zn
Structural highlights
FunctionQ5L0J3_GEOKA Required for replicative DNA synthesis. This DNA polymerase also exhibits 3' to 5' exonuclease activity (By similarity).[HAMAP-Rule:MF_00356][SAAS:SAAS029460_004_008054] 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 PubMedPolC is the polymerase responsible for genome duplication in many Gram-positive bacteria and represents an attractive target for antibacterial development. We have determined the 2.4-A resolution crystal structure of Geobacillus kaustophilus PolC in a ternary complex with DNA and dGTP. The structure reveals nascent base pair interactions that lead to highly accurate nucleotide incorporation. A unique beta-strand motif in the PolC thumb domain contacts the minor groove, allowing replication errors to be sensed up to 8 nt upstream of the active site. PolC exhibits the potential for large-scale conformational flexibility, which could encompass the catalytic residues. The structure suggests a mechanism by which the active site can communicate with the rest of the replisome to trigger proofreading after nucleotide misincorporation, leading to an integrated model for controlling the dynamic switch between replicative and repair polymerases. This ternary complex of a cellular replicative polymerase affords insights into polymerase fidelity, evolution, and structural diversity. Structure of PolC reveals unique DNA binding and fidelity determinants.,Evans RJ, Davies DR, Bullard JM, Christensen J, Green LS, Guiles JW, Pata JD, Ribble WK, Janjic N, Jarvis TC Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):20695-700. Epub 2008 Dec 23. PMID:19106298[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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