3f2b: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3f2b]] is a 3 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3F2B FirstGlance]. <br> | <table><tr><td colspan='2'>[[3f2b]] is a 3 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3F2B FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3f2c|3f2c]], [[3f2d|3f2d]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3f2c|3f2c]], [[3f2d|3f2d]]</td></tr> | ||
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GK1258, polC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 Geobacillus kaustophilus])</td></tr> | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GK1258, polC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 Geobacillus kaustophilus])</td></tr> | ||
<tr><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='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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3f2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f2b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3f2b RCSB], [http://www.ebi.ac.uk/pdbsum/3f2b PDBsum]</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=3f2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f2b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3f2b RCSB], [http://www.ebi.ac.uk/pdbsum/3f2b PDBsum]</span></td></tr> | ||
<table> | </table> | ||
== Function == | |||
[[http://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 == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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[[Category: DNA-directed DNA polymerase]] | [[Category: DNA-directed DNA polymerase]] | ||
[[Category: Geobacillus kaustophilus]] | [[Category: Geobacillus kaustophilus]] | ||
[[Category: Bullard, J M | [[Category: Bullard, J M]] | ||
[[Category: Christensen, J | [[Category: Christensen, J]] | ||
[[Category: Davies, D R | [[Category: Davies, D R]] | ||
[[Category: Evans, R J | [[Category: Evans, R J]] | ||
[[Category: Green, L S | [[Category: Green, L S]] | ||
[[Category: Guiles, J W | [[Category: Guiles, J W]] | ||
[[Category: Janjic, N | [[Category: Janjic, N]] | ||
[[Category: Jarvis, T C | [[Category: Jarvis, T C]] | ||
[[Category: Ribble, W K | [[Category: Ribble, W K]] | ||
[[Category: Dna polymerase c]] | [[Category: Dna polymerase c]] | ||
[[Category: Dna polymerase iii]] | [[Category: Dna polymerase iii]] | ||
Revision as of 01:31, 25 December 2014
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
Function[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 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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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)
OCA- DNA-directed DNA polymerase
- Geobacillus kaustophilus
- Bullard, J M
- Christensen, J
- Davies, D R
- Evans, R J
- Green, L S
- Guiles, J W
- Janjic, N
- Jarvis, T C
- Ribble, W K
- Dna polymerase c
- Dna polymerase iii
- Dna replication
- Dna-directed dna polymerase
- Exonuclease
- Hydrolase
- Nuclease
- Nucleotidyltransferase
- Protein-dna complex
- Replicative dna polymerase
- Ternary complex
- Transferase
- Transferase-dna complex