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1wns

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Revision as of 09:57, 26 May 2021

Crystal structure of family B DNA polymerase from hyperthermophilic archaeon pyrococcus kodakaraensis KOD1

Structural highlights

1wns is a 1 chain structure with sequence from Pyrococcus kodakaraensis (strain kod1). This structure supersedes the now removed PDB entry 1gcx. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	1tgo, 1qqc, 1qhc
Activity:	DNA-directed DNA polymerase, with EC number 2.7.7.7
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DPOL_PYRKO] Intein encoded endonucleases are thought to mediate intein mobility by site-specific recombination initiated by endonuclease cleavage at the "homing site" in gene that lack the intein. PI-PkoI recognizes 5'-GATTTAGATCCCTGTACC-3' and PI-PkoII recognizes 5'-CAGCTACTACGGTTAC-3'.

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

The crystal structure of family B DNA polymerase from the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 (KOD DNA polymerase) was determined. KOD DNA polymerase exhibits the highest known extension rate, processivity and fidelity. We carried out the structural analysis of KOD DNA polymerase in order to clarify the mechanisms of those enzymatic features. Structural comparison of DNA polymerases from hyperthermophilic archaea highlighted the conformational difference in Thumb domains. The Thumb domain of KOD DNA polymerase shows an "opened" conformation. The fingers subdomain possessed many basic residues at the side of the polymerase active site. The residues are considered to be accessible to the incoming dNTP by electrostatic interaction. A beta-hairpin motif (residues 242-249) extends from the Exonuclease (Exo) domain as seen in the editing complex of the RB69 DNA polymerase from bacteriophage RB69. Many arginine residues are located at the forked-point (the junction of the template-binding and editing clefts) of KOD DNA polymerase, suggesting that the basic environment is suitable for partitioning of the primer and template DNA duplex and for stabilizing the partially melted DNA structure in the high-temperature environments. The stabilization of the melted DNA structure at the forked-point may be correlated with the high PCR performance of KOD DNA polymerase, which is due to low error rate, high elongation rate and processivity.

Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1.,Hashimoto H, Nishioka M, Fujiwara S, Takagi M, Imanaka T, Inoue T, Kai Y J Mol Biol. 2001 Feb 23;306(3):469-77. PMID:11178906^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Hashimoto H, Nishioka M, Fujiwara S, Takagi M, Imanaka T, Inoue T, Kai Y. Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1. J Mol Biol. 2001 Feb 23;306(3):469-77. PMID:11178906 doi:10.1006/jmbi.2000.4403

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1wns"

@@ Line 3: / Line 3: @@
 <StructureSection load='1wns' size='340' side='right'caption='[[1wns]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1wns]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1gcx 1gcx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WNS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WNS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1wns]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1gcx 1gcx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WNS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WNS FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1tgo|1tgo]], [[1qqc|1qqc]], [[1qhc|1qhc]]</td></tr>
+</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1tgo|1tgo]], [[1qqc|1qqc]], [[1qhc|1qhc]]</div></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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://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=1wns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wns OCA], [http://pdbe.org/1wns PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wns RCSB], [http://www.ebi.ac.uk/pdbsum/1wns PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wns ProSAT]</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=1wns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wns OCA], [https://pdbe.org/1wns PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wns RCSB], [https://www.ebi.ac.uk/pdbsum/1wns PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wns ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DPOL_PYRKO DPOL_PYRKO]] Intein encoded endonucleases are thought to mediate intein mobility by site-specific recombination initiated by endonuclease cleavage at the "homing site" in gene that lack the intein. PI-PkoI recognizes 5'-GATTTAGATCCCTGTACC-3' and PI-PkoII recognizes 5'-CAGCTACTACGGTTAC-3'.
+[[https://www.uniprot.org/uniprot/DPOL_PYRKO DPOL_PYRKO]] Intein encoded endonucleases are thought to mediate intein mobility by site-specific recombination initiated by endonuclease cleavage at the "homing site" in gene that lack the intein. PI-PkoI recognizes 5'-GATTTAGATCCCTGTACC-3' and PI-PkoII recognizes 5'-CAGCTACTACGGTTAC-3'.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 29: / Line 29: @@
 </div>
 <div class="pdbe-citations 1wns" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 == References ==
 <references/>

1wns

From Proteopedia

Revision as of 09:57, 26 May 2021

Crystal structure of family B DNA polymerase from hyperthermophilic archaeon pyrococcus kodakaraensis KOD1

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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