2jgu

From Proteopedia

(Difference between revisions)

Revision as of 08:10, 19 January 2022

crystal structure of DNA-directed DNA polymerase

Structural highlights

2jgu is a 1 chain structure with sequence from Atcc 43587. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Activity:	DNA-directed DNA polymerase, with EC number 2.7.7.7
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DPOL_PYRFU] In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' 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

We have determined a 2.6A resolution crystal structure of Pfu DNA polymerase, the most commonly used high fidelity PCR enzyme, from Pyrococcus furiosus. Although the structures of Pfu and KOD1 are highly similar, the structure of Pfu elucidates the electron density of the interface between the exonuclease and thumb domains, which has not been previously observed in the KOD1 structure. The interaction of these two domains is known to coordinate the proofreading and polymerization activity of DNA polymerases, especially via H147 that is present within the loop (residues 144-158) of the exonuclease domain. In our structure of Pfu, however, E148 rather than H147 is located at better position to interact with the thumb domain. In addition, the structural analysis of Pfu and KOD1 shows that both the Y-GG/A and beta-hairpin motifs of Pfu are found to differ with that of KOD1, and may explain differences in processivity. This information enables us to better understand the mechanisms of polymerization and proofreading of DNA polymerases.

Crystal structure of Pfu, the high fidelity DNA polymerase from Pyrococcus furiosus.,Kim SW, Kim DU, Kim JK, Kang LW, Cho HS Int J Biol Macromol. 2008 May 1;42(4):356-61. Epub 2008 Feb 12. PMID:18355915^[1]

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

References

↑ Kim SW, Kim DU, Kim JK, Kang LW, Cho HS. Crystal structure of Pfu, the high fidelity DNA polymerase from Pyrococcus furiosus. Int J Biol Macromol. 2008 May 1;42(4):356-61. Epub 2008 Feb 12. PMID:18355915 doi:10.1016/j.ijbiomac.2008.01.010

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/2jgu"

@@ Line 3: / Line 3: @@
 <StructureSection load='2jgu' size='340' side='right'caption='[[2jgu]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2jgu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JGU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2JGU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2jgu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JGU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JGU FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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='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://proteopedia.org/fgij/fg.htm?mol=2jgu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jgu OCA], [http://pdbe.org/2jgu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jgu RCSB], [http://www.ebi.ac.uk/pdbsum/2jgu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2jgu 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=2jgu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jgu OCA], [https://pdbe.org/2jgu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jgu RCSB], [https://www.ebi.ac.uk/pdbsum/2jgu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jgu ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DPOL_PYRFU DPOL_PYRFU]] In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity.
+[[https://www.uniprot.org/uniprot/DPOL_PYRFU DPOL_PYRFU]] In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 29: / Line 29: @@
 </div>
 <div class="pdbe-citations 2jgu" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 == References ==
 <references/>

2jgu

From Proteopedia

Revision as of 08:10, 19 January 2022

crystal structure of DNA-directed DNA polymerase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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