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.


1njw

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:21, 16 August 2023) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1njw.png|left|200px]]
 
-
{{STRUCTURE_1njw| PDB=1njw | SCENE= }}
+
==GUANINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE==
 +
<StructureSection load='1njw' size='340' side='right'caption='[[1njw]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1njw]] 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=1NJW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NJW FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#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>
 +
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1njw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njw OCA], [https://pdbe.org/1njw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1njw RCSB], [https://www.ebi.ac.uk/pdbsum/1njw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1njw ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q5KWC1_GEOKA Q5KWC1_GEOKA]
 +
== 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/nj/1njw_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=1njw 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.
-
===GUANINE-THYMINE 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>
-
{{ABSTRACT_PUBMED_15035983}}
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
==About this Structure==
+
<div class="pdbe-citations 1njw" style="background-color:#fffaf0;"></div>
-
[[1njw]] is a 3 chain structure 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=1NJW OCA].
+
==See Also==
==See Also==
-
*[[DNA polymerase|DNA polymerase]]
+
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:015035983</ref><ref group="xtra">PMID:012649320</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

GUANINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE

PDB ID 1njw

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/1njw"
Personal tools