4esv: Difference between revisions
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New page: '''Unreleased structure''' The entry 4esv is ON HOLD Authors: Itsathitphaisarn, O., Wing, R.A., Eliason, W.K., Wang, J., Steitz, T.A. Description: A New Twist on The Translocation Mech... |
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The | ==A New Twist on the Translocation Mechanism of Helicases from the Structure of DnaB with its Substrates== | ||
<StructureSection load='4esv' size='340' side='right'caption='[[4esv]], [[Resolution|resolution]] 3.20Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4esv]] is a 14 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. The December 2013 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''DNA Helicase'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2013_12 10.2210/rcsb_pdb/mom_2013_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ESV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ESV FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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=4esv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4esv OCA], [https://pdbe.org/4esv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4esv RCSB], [https://www.ebi.ac.uk/pdbsum/4esv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4esv ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/DNAB_GEOSE DNAB_GEOSE] The main replicative DNA helicase, it participates in initiation and elongation during chromosome replication. Travels ahead of the DNA replisome, separating double-stranded (ds)DNA into templates for DNA synthesis. Binding of single-stranded (ss)DNA to the hexamer suggests a 2-nucleotide step size for the helicase and a hand-over-hand mechanism of DNA unwinding (Probable) (PubMed:23022319). Has ssDNA-stimulated ATPase activity (PubMed:10625492). DnaG primase stimulates the helicase activity (the helicase direction was not determine but is probably 5'-3') (PubMed:10625492, PubMed:12235389, PubMed:23022319). Loaded onto DNA by helicase loader DnaI (shown with DnaI of B.subtilis); ATP-binding enhances loading and subsequent ATP hydrolysis dissociates the complex, leaving helicase on the DNA (PubMed:17003052). Binds ssDNA and less well dsDNA, in the presence of ADPNP (probably 5'-adenylyl beta, gamma-imidodiphosphate, but not ATP) binding to both DNAs is improved (PubMed:12235389, PubMed:17003052).<ref>PMID:10625492</ref> <ref>PMID:12235389</ref> <ref>PMID:17003052</ref> <ref>PMID:23022319</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
DNA polymerases can only synthesize nascent DNA from single-stranded DNA (ssDNA) templates. In bacteria, the unwinding of parental duplex DNA is carried out by the replicative DNA helicase (DnaB) that couples NTP hydrolysis to 5' to 3' translocation. The crystal structure of the DnaB hexamer in complex with GDP-AlF(4) and ssDNA reported here reveals that DnaB adopts a closed spiral staircase quaternary structure around an A-form ssDNA with each C-terminal domain coordinating two nucleotides of ssDNA. The structure not only provides structural insights into the translocation mechanism of superfamily IV helicases but also suggests that members of this superfamily employ a translocation mechanism that is distinct from other helicase superfamilies. We propose a hand-over-hand mechanism in which sequential hydrolysis of NTP causes a sequential 5' to 3' movement of the subunits along the helical axis of the staircase, resulting in the unwinding of two nucleotides per subunit. | |||
The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation.,Itsathitphaisarn O, Wing RA, Eliason WK, Wang J, Steitz TA Cell. 2012 Oct 12;151(2):267-77. doi: 10.1016/j.cell.2012.09.014. Epub 2012 Sep, 27. PMID:23022319<ref>PMID:23022319</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4esv" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Helicase 3D structures|Helicase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: DNA Helicase]] | |||
[[Category: Geobacillus stearothermophilus]] | |||
[[Category: Large Structures]] | |||
[[Category: RCSB PDB Molecule of the Month]] | |||
[[Category: Synthetic construct]] | |||
[[Category: Eliason WK]] | |||
[[Category: Itsathitphaisarn O]] | |||
[[Category: Steitz TA]] | |||
[[Category: Wang J]] | |||
[[Category: Wing RA]] | |||
Latest revision as of 10:52, 13 August 2026
A New Twist on the Translocation Mechanism of Helicases from the Structure of DnaB with its Substrates
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