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.


5j0r

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:36, 6 March 2024) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
==Binary complex crystal structure of DNA polymerase Beta with C:A mismatch at the primer terminus==
==Binary complex crystal structure of DNA polymerase Beta with C:A mismatch at the primer terminus==
-
<StructureSection load='5j0r' size='340' side='right' caption='[[5j0r]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+
<StructureSection load='5j0r' size='340' side='right'caption='[[5j0r]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[5j0r]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J0R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J0R FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[5j0r]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J0R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J0R FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.001&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5j0o|5j0o]], [[5j0p|5j0p]], [[5j0q|5j0q]], [[5j0s|5j0s]], [[5j0t|5j0t]], [[5j0u|5j0u]], [[5j0v|5j0v]], [[5j0w|5j0w]], [[5j0x|5j0x]], [[5j0y|5j0y]], [[5j29|5j29]], [[5j2a|5j2a]], [[5j2b|5j2b]], [[5j2c|5j2c]], [[5j2d|5j2d]], [[5j2e|5j2e]], [[5j2f|5j2f]], [[5j2g|5j2g]], [[5j2h|5j2h]], [[5j2i|5j2i]], [[5j2j|5j2j]], [[5j2k|5j2k]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5j0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j0r OCA], [http://pdbe.org/5j0r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j0r RCSB], [http://www.ebi.ac.uk/pdbsum/5j0r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j0r 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=5j0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j0r OCA], [https://pdbe.org/5j0r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j0r RCSB], [https://www.ebi.ac.uk/pdbsum/5j0r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j0r ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN]] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
+
[https://www.uniprot.org/uniprot/DPOLB_HUMAN DPOLB_HUMAN] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.<ref>PMID:9207062</ref> <ref>PMID:9572863</ref> <ref>PMID:11805079</ref> <ref>PMID:21362556</ref>
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
High-fidelity DNA synthesis requires that polymerases display a strong preference for right nucleotide insertion. When the wrong nucleotide is inserted, the polymerase deters extension from the mismatched DNA terminus. Twenty-three crystallographic structures of DNA polymerase beta with terminal template-primer mismatches were determined as binary DNA and ternary pre-catalytic substrate complexes. These structures indicate that the mismatched termini adopt various distorted conformations that attempt to satisfy stacking and hydrogen-bonding interactions. The binary complex structures indicate an induced strain in the mismatched template nucleotide. Addition of a non-hydrolyzable incoming nucleotide stabilizes the templating nucleotide with concomitant strain in the primer terminus. Several dead-end ternary complex structures suggest that DNA synthesis might occur as the enzyme transitions from an open to a closed complex. The structures are consistent with an induced-fit mechanism where a mismatched terminus is misaligned relative to the correct incoming nucleotide to deter or delay further DNA synthesis.
+
-
Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism.,Batra VK, Beard WA, Pedersen LC, Wilson SH Structure. 2016 Sep 13. pii: S0969-2126(16)30238-6. doi:, 10.1016/j.str.2016.08.006. PMID:27642161<ref>PMID:27642161</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 5j0r" style="background-color:#fffaf0;"></div>
+
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Batra, V K]]
+
[[Category: Homo sapiens]]
-
[[Category: Wilson, S H]]
+
[[Category: Large Structures]]
-
[[Category: Binary complex]]
+
[[Category: Synthetic construct]]
-
[[Category: Dna polymerase beta]]
+
[[Category: Batra VK]]
-
[[Category: Mismatch extension]]
+
[[Category: Wilson SH]]
-
[[Category: Transferase-dna complex]]
+

Current revision

Binary complex crystal structure of DNA polymerase Beta with C:A mismatch at the primer terminus

PDB ID 5j0r

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/5j0r"
Personal tools