4hyk: Difference between revisions

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 ==Dbh Ternary Complex (substrates partially disordered)==
-<StructureSection load='4hyk' size='340' side='right' caption='[[4hyk]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='4hyk' size='340' side='right'caption='[[4hyk]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4hyk]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius_dsm_639 Sulfolobus acidocaldarius dsm 639]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HYK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HYK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4hyk]] is a 3 chain structure with sequence from [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=4HYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HYK FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4f4w|4f4w]], [[4f4x|4f4x]], [[4f4y|4f4y]], [[4f4z|4f4z]], [[4f50|4f50]]</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]] 2.802&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dbh, Saci_0554 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=330779 Sulfolobus acidocaldarius DSM 639])</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=4hyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hyk OCA], [https://pdbe.org/4hyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hyk RCSB], [https://www.ebi.ac.uk/pdbsum/4hyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hyk 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=4hyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hyk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4hyk RCSB], [http://www.ebi.ac.uk/pdbsum/4hyk PDBsum]</span></td></tr>
 </table>
 == 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_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==
-*[[DNA polymerase|DNA polymerase]]
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: DNA-directed DNA polymerase]]
+[[Category: Large Structures]]
-[[Category: Sulfolobus acidocaldarius dsm 639]]
+[[Category: Sulfolobus acidocaldarius DSM 639]]
-[[Category: Pata, J D]]
+[[Category: Synthetic construct]]
-[[Category: Wilson, R C]]
+[[Category: Pata JD]]
-[[Category: Transferase-dna complex]]
+[[Category: Wilson RC]]
-[[Category: Y-family dna polymerase]]