1d5a: Difference between revisions

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<StructureSection load='1d5a' size='340' side='right'caption='[[1d5a]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
<StructureSection load='1d5a' size='340' side='right'caption='[[1d5a]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1d5a]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desst Desst]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D5A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D5A FirstGlance]. <br>
<table><tr><td colspan='2'>[[1d5a]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfurococcus_sp._Tok Desulfurococcus sp. Tok]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D5A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D5A FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qqc|1qqc]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=1d5a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d5a OCA], [https://pdbe.org/1d5a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d5a RCSB], [https://www.ebi.ac.uk/pdbsum/1d5a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d5a 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=1d5a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d5a OCA], [https://pdbe.org/1d5a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d5a RCSB], [https://www.ebi.ac.uk/pdbsum/1d5a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d5a ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/DPOL_DESST DPOL_DESST]] Thermostable DNA polymerase. In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity.<ref>PMID:8663453</ref>
[https://www.uniprot.org/uniprot/DPOL_DESST DPOL_DESST] Thermostable DNA polymerase. In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity.<ref>PMID:8663453</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1d5a ConSurf].
</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=1d5a ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
BACKGROUND: Members of the Pol II family of DNA polymerases are responsible for chromosomal replication in eukaryotes, and carry out highly processive DNA replication when attached to ring-shaped processivity clamps. The sequences of Pol II polymerases are distinct from those of members of the well-studied Pol I family of DNA polymerases. The DNA polymerase from the archaebacterium Desulfurococcus strain Tok (D. Tok Pol) is a member of the Pol II family that retains catalytic activity at elevated temperatures. RESULTS: The crystal structure of D. Tok Pol has been determined at 2.4 A resolution. The architecture of this Pol II type DNA polymerase resembles that of the DNA polymerase from the bacteriophage RB69, with which it shares less than approximately 20% sequence identity. As in RB69, the central catalytic region of the DNA polymerase is located within the 'palm' subdomain and is strikingly similar in structure to the corresponding regions of Pol I type DNA polymerases. The structural scaffold that surrounds the catalytic core in D. Tok Pol is unrelated in structure to that of Pol I type polymerases. The 3'-5' proofreading exonuclease domain of D. Tok Pol resembles the corresponding domains of RB69 Pol and Pol I type DNA polymerases. The exonuclease domain in D. Tok Pol is located in the same position relative to the polymerase domain as seen in RB69, and on the opposite side of the palm subdomain compared to its location in Pol I type polymerases. The N-terminal domain of D. Tok Pol has structural similarity to RNA-binding domains. Sequence alignments suggest that this domain is conserved in the eukaryotic DNA polymerases delta and epsilon. CONCLUSIONS: The structure of D. Tok Pol confirms that the modes of binding of the template and extrusion of newly synthesized duplex DNA are likely to be similar in both Pol II and Pol I type DNA polymerases. However, the mechanism by which the newly synthesized product transits in and out of the proofreading exonuclease domain has to be quite different. The discovery of a domain that seems to be an RNA-binding module raises the possibility that Pol II family members interact with RNA.


Crystal structure of an archaebacterial DNA polymerase.,Zhao Y, Jeruzalmi D, Moarefi I, Leighton L, Lasken R, Kuriyan J Structure. 1999 Oct 15;7(10):1189-99. PMID:10545321<ref>PMID:10545321</ref>
==See Also==
 
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1d5a" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: DNA-directed DNA polymerase]]
[[Category: Desulfurococcus sp. Tok]]
[[Category: Desst]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Jeruzalmi, D]]
[[Category: Jeruzalmi D]]
[[Category: Kuriyan, J]]
[[Category: Kuriyan J]]
[[Category: Lasken, R]]
[[Category: Lasken R]]
[[Category: Leighton, L]]
[[Category: Leighton L]]
[[Category: Zhao, Y]]
[[Category: Zhao Y]]
[[Category: Dna polymerase]]
[[Category: Exonuclease]]
[[Category: Rbd domain]]
[[Category: Thermostable]]
[[Category: Transferase]]

Revision as of 18:46, 13 March 2024

CRYSTAL STRUCTURE OF AN ARCHAEBACTERIAL DNA POLYMERASE D.TOK. DEPOSITION OF SECOND NATIVE STRUCTURE AT 2.4 ANGSTROMCRYSTAL STRUCTURE OF AN ARCHAEBACTERIAL DNA POLYMERASE D.TOK. DEPOSITION OF SECOND NATIVE STRUCTURE AT 2.4 ANGSTROM

Structural highlights

1d5a is a 1 chain structure with sequence from Desulfurococcus sp. Tok. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPOL_DESST Thermostable DNA polymerase. In addition to polymerase activity, this DNA polymerase exhibits 3' to 5' exonuclease activity.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Lasken RS, Schuster DM, Rashtchian A. Archaebacterial DNA polymerases tightly bind uracil-containing DNA. J Biol Chem. 1996 Jul 26;271(30):17692-6. PMID:8663453

1d5a, resolution 2.40Å

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