4f4y: Difference between revisions

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==Y-family DNA polymerase chimera Dbh-Dpo4-Dbh==
==Y-family DNA polymerase chimera Dbh-Dpo4-Dbh==
<StructureSection load='4f4y' size='340' side='right' caption='[[4f4y]], [[Resolution|resolution]] 2.34&Aring;' scene=''>
<StructureSection load='4f4y' size='340' side='right'caption='[[4f4y]], [[Resolution|resolution]] 2.34&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4f4y]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulac Sulac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F4Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4F4Y FirstGlance]. <br>
<table><tr><td colspan='2'>[[4f4y]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2], [https://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius_DSM_639 Sulfolobus acidocaldarius DSM 639] 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=4F4Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4F4Y FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 2.338&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4f4w|4f4w]], [[4f4x|4f4x]], [[4f4z|4f4z]], [[4f50|4f50]]</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 (S. solfataricus) and Dbh (S. acidocaldarius), Saci_0554, dpo4, SSO2448 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=330779 SULAC])</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=4f4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f4y OCA], [https://pdbe.org/4f4y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4f4y RCSB], [https://www.ebi.ac.uk/pdbsum/4f4y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4f4y ProSAT]</span></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></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=4f4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f4y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4f4y RCSB], [http://www.ebi.ac.uk/pdbsum/4f4y PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/DPO4_SULAC DPO4_SULAC]] 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. May be involved in translesional synthesis (By similarity).  
[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.[https://www.uniprot.org/uniprot/DPO4_SULAC DPO4_SULAC] 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. May be involved in translesional synthesis (By similarity).
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Y-family polymerases help cells tolerate DNA damage by performing translesion synthesis opposite damaged DNA bases, yet they also have a high intrinsic error rate. We constructed chimeras of two closely related Y-family polymerases that display distinctly different activity profiles and found that the polypeptide linker that tethers the catalytic polymerase domain to the C-terminal DNA-binding domain is a major determinant of overall polymerase activity, nucleotide incorporation fidelity, and abasic site-bypass ability. Exchanging just 3 out of the 15 linker residues is sufficient to interconvert the polymerase activities tested. Crystal structures of four chimeras show that the conformation of the protein correlates with the identity of the interdomain linker sequence. Thus, residues that are more than 15 A away from the active site are able to influence many aspects of polymerase activity by altering the relative orientations of the catalytic and DNA-binding domains.
 
Y-Family Polymerase Conformation Is a Major Determinant of Fidelity and Translesion Specificity.,Wilson RC, Jackson MA, Pata JD Structure. 2012 Dec 11. pii: S0969-2126(12)00420-0. doi:, 10.1016/j.str.2012.11.005. PMID:23245850<ref>PMID:23245850</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[DNA polymerase|DNA polymerase]]
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: DNA-directed DNA polymerase]]
[[Category: Large Structures]]
[[Category: Sulac]]
[[Category: Saccharolobus solfataricus P2]]
[[Category: Pata, J D]]
[[Category: Sulfolobus acidocaldarius DSM 639]]
[[Category: Wilson, R C]]
[[Category: Synthetic construct]]
[[Category: Transferase-dna complex]]
[[Category: Pata JD]]
[[Category: Y-family polymerase]]
[[Category: Wilson RC]]

Latest revision as of 14:10, 1 March 2024

Y-family DNA polymerase chimera Dbh-Dpo4-DbhY-family DNA polymerase chimera Dbh-Dpo4-Dbh

Structural highlights

4f4y is a 6 chain structure with sequence from Saccharolobus solfataricus P2, Sulfolobus acidocaldarius DSM 639 and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.338Å
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.DPO4_SULAC 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. May be involved in translesional synthesis (By similarity).

See Also

4f4y, resolution 2.34Å

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