1nk5

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "1nk5" [edit=sysop:move=sysop])
Current revision (09:21, 16 August 2023) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1nk5.png|left|200px]]
 
-
<!--
+
==ADENINE-ADENINE MISMATCH AT THE POLYMERASE ACTIVE SITE==
-
The line below this paragraph, containing "STRUCTURE_1nk5", creates the "Structure Box" on the page.
+
<StructureSection load='1nk5' size='340' side='right'caption='[[1nk5]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1nk5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NK5 FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
{{STRUCTURE_1nk5| PDB=1nk5 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nk5 OCA], [https://pdbe.org/1nk5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nk5 RCSB], [https://www.ebi.ac.uk/pdbsum/1nk5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nk5 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/DPO1_GEOSE DPO1_GEOSE] In addition to polymerase activity, this DNA polymerase exhibits 5' to 3' exonuclease activity.
 +
== 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/nk/1nk5_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=1nk5 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Accurate DNA replication is essential for genomic stability. One mechanism by which high-fidelity DNA polymerases maintain replication accuracy involves stalling of the polymerase in response to covalent incorporation of mismatched base pairs, thereby favoring subsequent mismatch excision. Some polymerases retain a "short-term memory" of replication errors, responding to mismatches up to four base pairs in from the primer terminus. Here we a present a structural characterization of all 12 possible mismatches captured at the growing primer terminus in the active site of a polymerase. Our observations suggest four mechanisms that lead to mismatch-induced stalling of the polymerase. Furthermore, we have observed the effects of extending a mismatch up to six base pairs from the primer terminus and find that long-range distortions in the DNA transmit the presence of the mismatch back to the enzyme active site, suggesting the structural basis for the short-term memory of replication errors.
-
===ADENINE-ADENINE MISMATCH AT THE POLYMERASE ACTIVE SITE===
+
Structures of mismatch replication errors observed in a DNA polymerase.,Johnson SJ, Beese LS Cell. 2004 Mar 19;116(6):803-16. PMID:15035983<ref>PMID:15035983</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_15035983}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 1nk5" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 15035983 is the PubMed ID number.
+
-
-->
+
-
{{ABSTRACT_PUBMED_15035983}}
+
-
 
+
-
==About this Structure==
+
-
[[1nk5]] is a 3 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NK5 OCA].
+
==See Also==
==See Also==
-
*[[DNA polymerase]]
+
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:15035983</ref><ref group="xtra">PMID:12649320</ref><references group="xtra"/>
+
__TOC__
-
[[Category: DNA-directed DNA polymerase]]
+
</StructureSection>
[[Category: Geobacillus stearothermophilus]]
[[Category: Geobacillus stearothermophilus]]
-
[[Category: Beese, L S.]]
+
[[Category: Large Structures]]
-
[[Category: Johnson, S J.]]
+
[[Category: Beese LS]]
-
[[Category: Dna mismatch]]
+
[[Category: Johnson SJ]]
-
[[Category: Dna polymerase i]]
+
-
[[Category: Dna replication]]
+
-
[[Category: Klenow fragment]]
+
-
[[Category: Protein-dna complex]]
+
-
[[Category: Transferase/dna complex]]
+

Current revision

ADENINE-ADENINE MISMATCH AT THE POLYMERASE ACTIVE SITE

PDB ID 1nk5

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/1nk5"
Personal tools