This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1qqc

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:06, 17 April 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1qqc.gif|left|200px]]
 
-
{{Structure
+
==CRYSTAL STRUCTURE OF AN ARCHAEBACTERIAL DNA POLYMERASE D.TOK==
-
|PDB= 1qqc |SIZE=350|CAPTION= <scene name='initialview01'>1qqc</scene>, resolution 2.6&Aring;
+
<StructureSection load='1qqc' size='340' side='right'caption='[[1qqc]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene>
+
<table><tr><td colspan='2'>[[1qqc]] 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=1QQC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QQC FirstGlance]. <br>
-
|ACTIVITY= [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]
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
-
|GENE=
+
<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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qqc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qqc OCA], [https://pdbe.org/1qqc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qqc RCSB], [https://www.ebi.ac.uk/pdbsum/1qqc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qqc ProSAT]</span></td></tr>
 +
</table>
 +
== 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>
 +
== 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/qq/1qqc_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=1qqc ConSurf].
 +
<div style="clear:both"></div>
-
'''CRYSTAL STRUCTURE OF AN ARCHAEBACTERIAL DNA POLYMERASE D.TOK'''
+
==See Also==
-
 
+
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-
 
+
== References ==
-
==Overview==
+
<references/>
-
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.
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Desulfurococcus sp. Tok]]
-
1QQC is a [[Single protein]] structure of sequence from [http://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=1QQC OCA].
+
[[Category: Large Structures]]
-
 
+
[[Category: Jeruzalmi D]]
-
==Reference==
+
[[Category: Kuriyan J]]
-
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:[http://www.ncbi.nlm.nih.gov/pubmed/10545321 10545321]
+
[[Category: Lasken R]]
-
[[Category: DNA-directed DNA polymerase]]
+
[[Category: Leighton L]]
-
[[Category: Desulfurococcus sp. tok]]
+
[[Category: Zhao Y]]
-
[[Category: Single protein]]
+
-
[[Category: Jeruzalmi, D.]]
+
-
[[Category: Kuriyan, J.]]
+
-
[[Category: Lasken, R.]]
+
-
[[Category: Leighton, L.]]
+
-
[[Category: Zhao, Y.]]
+
-
[[Category: MG]]
+
-
[[Category: SO4]]
+
-
[[Category: dna polymerase]]
+
-
[[Category: exonuclease]]
+
-
[[Category: rbd domain]]
+
-
[[Category: thermostable]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:41:18 2008''
+

Current revision

CRYSTAL STRUCTURE OF AN ARCHAEBACTERIAL DNA POLYMERASE D.TOK

PDB ID 1qqc

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1qqc"
Personal tools