6s3h: Difference between revisions
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==== | ==Crystal structure of helicase Pif1 from Thermus oshimai in complex with ADP-AlF4 and (dT)7ds11bp== | ||
<StructureSection load='6s3h' size='340' side='right'caption='[[6s3h]]' scene=''> | <StructureSection load='6s3h' size='340' side='right'caption='[[6s3h]], [[Resolution|resolution]] 2.06Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br> | <table><tr><td colspan='2'>[[6s3h]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_oshimai Thermus oshimai] and [https://en.wikipedia.org/wiki/Thermus_oshimai_JL-2 Thermus oshimai JL-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S3H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6S3H FirstGlance]. <br> | ||
</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=6s3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s3h OCA], [https://pdbe.org/6s3h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6s3h RCSB], [https://www.ebi.ac.uk/pdbsum/6s3h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6s3h ProSAT]</span></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]] 2.06Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6s3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s3h OCA], [https://pdbe.org/6s3h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6s3h RCSB], [https://www.ebi.ac.uk/pdbsum/6s3h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6s3h ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/K7RJ88_THEOS K7RJ88_THEOS] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Pif1 is an SF1B helicase that is evolutionarily conserved from bacteria to humans and plays multiple roles in maintaining genome stability in both nucleus and mitochondria. Though highly conserved, Pif1 family harbors a large mechanistic diversity. Here, we report crystal structures of Thermus oshimai Pif1 (ToPif1) alone and complexed with partial duplex or single-stranded DNA. In the apo state and in complex with a partial duplex DNA, ToPif1 is monomeric with its domain 2B/loop3 adopting a closed and an open conformation, respectively. When complexed with a single-stranded DNA, ToPif1 forms a stable dimer with domain 2B/loop3 shifting to a more open conformation. Single-molecule and biochemical assays show that domain 2B/loop3 switches repetitively between the closed and open conformations when a ToPif1 monomer unwinds DNA and, in contrast with other typical dimeric SF1A helicases, dimerization has an inhibitory effect on its helicase activity. This mechanism is not general for all Pif1 helicases but illustrates the diversity of regulation mechanisms among different helicases. It also raises the possibility that although dimerization results in activation for SF1A helicases, it may lead to inhibition for some of the other uncharacterized SF1B helicases, an interesting subject warranting further studies. | |||
Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition.,Dai YX, Chen WF, Liu NN, Teng FY, Guo HL, Hou XM, Dou SX, Rety S, Xi XG Nucleic Acids Res. 2021 Mar 30. pii: 6204648. doi: 10.1093/nar/gkab188. PMID:33784404<ref>PMID:33784404</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6s3h" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Helicase 3D structures|Helicase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Thermus oshimai]] | ||
[[Category: Thermus oshimai JL-2]] | |||
[[Category: Chen WF]] | |||
[[Category: Dai YX]] | |||
[[Category: Dou SX]] | |||
[[Category: Hou XM]] | |||
[[Category: Liu NN]] | |||
[[Category: Rety S]] | |||
[[Category: Teng FY]] | |||
[[Category: Xi XG]] | |||
Latest revision as of 15:34, 24 January 2024
Crystal structure of helicase Pif1 from Thermus oshimai in complex with ADP-AlF4 and (dT)7ds11bpCrystal structure of helicase Pif1 from Thermus oshimai in complex with ADP-AlF4 and (dT)7ds11bp
Structural highlights
FunctionPublication Abstract from PubMedPif1 is an SF1B helicase that is evolutionarily conserved from bacteria to humans and plays multiple roles in maintaining genome stability in both nucleus and mitochondria. Though highly conserved, Pif1 family harbors a large mechanistic diversity. Here, we report crystal structures of Thermus oshimai Pif1 (ToPif1) alone and complexed with partial duplex or single-stranded DNA. In the apo state and in complex with a partial duplex DNA, ToPif1 is monomeric with its domain 2B/loop3 adopting a closed and an open conformation, respectively. When complexed with a single-stranded DNA, ToPif1 forms a stable dimer with domain 2B/loop3 shifting to a more open conformation. Single-molecule and biochemical assays show that domain 2B/loop3 switches repetitively between the closed and open conformations when a ToPif1 monomer unwinds DNA and, in contrast with other typical dimeric SF1A helicases, dimerization has an inhibitory effect on its helicase activity. This mechanism is not general for all Pif1 helicases but illustrates the diversity of regulation mechanisms among different helicases. It also raises the possibility that although dimerization results in activation for SF1A helicases, it may lead to inhibition for some of the other uncharacterized SF1B helicases, an interesting subject warranting further studies. Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition.,Dai YX, Chen WF, Liu NN, Teng FY, Guo HL, Hou XM, Dou SX, Rety S, Xi XG Nucleic Acids Res. 2021 Mar 30. pii: 6204648. doi: 10.1093/nar/gkab188. PMID:33784404[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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