3qz8: Difference between revisions

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<StructureSection load='3qz8' size='340' side='right'caption='[[3qz8]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3qz8' size='340' side='right'caption='[[3qz8]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3qz8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_35091 Atcc 35091]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QZ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QZ8 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3qz8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QZ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QZ8 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</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]] 1.999&#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;'>[[3qz7|3qz7]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dbh, dpo4, SSO2448 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ATCC 35091])</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=3qz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qz8 OCA], [https://pdbe.org/3qz8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qz8 RCSB], [https://www.ebi.ac.uk/pdbsum/3qz8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qz8 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=3qz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qz8 OCA], [https://pdbe.org/3qz8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qz8 RCSB], [https://www.ebi.ac.uk/pdbsum/3qz8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qz8 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/DPO4_SULSO DPO4_SULSO]] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. It is involved in translesional synthesis.[HAMAP-Rule:MF_01113]
[https://www.uniprot.org/uniprot/DPO4_SACS2 DPO4_SACS2] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. It is involved in translesional synthesis.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The Y-family polymerases help cells tolerate DNA damage by performing translesion synthesis, yet they also can be highly error-prone. One distinctive feature of the DinB class of Y-family polymerases is that they make single-base deletion errors at high frequencies in repetitive sequences, especially those that contain two or more identical pyrimidines with a 5' flanking guanosine. Intriguingly, different deletion mechanisms have been proposed even for two archaeal DinB polymerases that share 54% sequence identity and originate from two strains of Sulfolobus. To reconcile these apparent differences, we have characterized Dpo4 from S. solfataricus using the same biochemical and crystallographic approaches that we have used previously to characterize Dbh from S. acidocaldarius. In contrast to previous suggestions that Dpo4 uses a dNTP-stabilized misalignment mechanism when creating single-base deletions, we find that Dpo4 predominantly uses a template-slippage deletion mechanism when replicating repetitive DNA sequences, as was previously shown for Dbh. Dpo4 stabilizes the skipped template base in an extrahelical conformation between the polymerase and the little-finger domains of the enzyme. This contrasts with Dbh, where the extrahelical base is stabilized against the surface of little-finger domain alone. Thus, despite sharing a common deletion mechanism, these closely related polymerases use different contacts with the substrate to accomplish the same result.


The Y-family DNA polymerase Dpo4 uses a template-slippage mechanism to create single-base deletions.,Wu Y, Wilson RC, Pata JD J Bacteriol. 2011 Mar 18. PMID:21421759<ref>PMID:21421759</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 3qz8" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 35091]]
[[Category: DNA-directed DNA polymerase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Pata, J D]]
[[Category: Saccharolobus solfataricus]]
[[Category: Wilson, R C]]
[[Category: Pata JD]]
[[Category: Wu, Y]]
[[Category: Wilson RC]]
[[Category: Frameshift]]
[[Category: Wu Y]]
[[Category: Lesion bypass]]
[[Category: Replication-dna complex]]
[[Category: Single-base deletion]]
[[Category: Transferase-dna complex]]

Latest revision as of 15:03, 14 March 2024

TT-4 ternary complex of Dpo4TT-4 ternary complex of Dpo4

Structural highlights

3qz8 is a 3 chain structure with sequence from Saccharolobus solfataricus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.999Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPO4_SACS2 Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. It is involved in translesional synthesis.

See Also

3qz8, resolution 2.00Å

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