9p9a: Difference between revisions

Latest revision as of 04:45, 24 June 2026

DnaB complex binding with ssDNA and dTDP-AlFx

Structural highlights

9p9a is a 7 chain structure with sequence from Geobacillus stearothermophilus and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.5Å
Ligands:	ALF, MG, TYD
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2] ^[3] ^[4]

References

↑ Bird LE, Pan H, Soultanas P, Wigley DB. Mapping protein-protein interactions within a stable complex of DNA primase and DnaB helicase from Bacillus stearothermophilus. Biochemistry. 2000 Jan 11;39(1):171-82. PMID:10625492 doi:10.1021/bi9918801
↑ Soultanas P, Wigley DB. Site-directed mutagenesis reveals roles for conserved amino acid residues in the hexameric DNA helicase DnaB from Bacillus stearothermophilus. Nucleic Acids Res. 2002 Sep 15;30(18):4051-60. PMID:12235389 doi:10.1093/nar/gkf527
↑ Ioannou C, Schaeffer PM, Dixon NE, Soultanas P. Helicase binding to DnaI exposes a cryptic DNA-binding site during helicase loading in Bacillus subtilis. Nucleic Acids Res. 2006;34(18):5247-58. PMID:17003052 doi:10.1093/nar/gkl690
↑ Itsathitphaisarn O, Wing RA, Eliason WK, Wang J, Steitz TA. The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation. Cell. 2012 Oct 12;151(2):267-77. doi: 10.1016/j.cell.2012.09.014. Epub 2012 Sep, 27. PMID:23022319 doi:https://dx.doi.org/10.1016/j.cell.2012.09.014

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OCA

[1] Bird LE, Pan H, Soultanas P, Wigley DB. Mapping protein-protein interactions within a stable complex of DNA primase and DnaB helicase from Bacillus stearothermophilus. Biochemistry. 2000 Jan 11;39(1):171-82. PMID:10625492 doi:10.1021/bi9918801

[2] Soultanas P, Wigley DB. Site-directed mutagenesis reveals roles for conserved amino acid residues in the hexameric DNA helicase DnaB from Bacillus stearothermophilus. Nucleic Acids Res. 2002 Sep 15;30(18):4051-60. PMID:12235389 doi:10.1093/nar/gkf527

[3] Ioannou C, Schaeffer PM, Dixon NE, Soultanas P. Helicase binding to DnaI exposes a cryptic DNA-binding site during helicase loading in Bacillus subtilis. Nucleic Acids Res. 2006;34(18):5247-58. PMID:17003052 doi:10.1093/nar/gkl690

[4] Itsathitphaisarn O, Wing RA, Eliason WK, Wang J, Steitz TA. The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation. Cell. 2012 Oct 12;151(2):267-77. doi: 10.1016/j.cell.2012.09.014. Epub 2012 Sep, 27. PMID:23022319 doi:https://dx.doi.org/10.1016/j.cell.2012.09.014

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[2]

[3]

[4]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9p9a is ON HOLD  until Paper Publication
+==DnaB complex binding with ssDNA and dTDP-AlFx==
+<StructureSection load='9p9a' size='340' side='right'caption='[[9p9a]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
-Authors:
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9p9a]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] 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=9P9A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9P9A FirstGlance]. <br>
-Description:
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.5&#8491;</td></tr>
-[[Category: Unreleased Structures]]
+<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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</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=9p9a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9p9a OCA], [https://pdbe.org/9p9a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9p9a RCSB], [https://www.ebi.ac.uk/pdbsum/9p9a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9p9a 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>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Geobacillus stearothermophilus]]
+[[Category: Large Structures]]
+[[Category: Synthetic construct]]
+[[Category: Berger JM]]
+[[Category: Liu C]]

9p9a: Difference between revisions

Latest revision as of 04:45, 24 June 2026

DnaB complex binding with ssDNA and dTDP-AlFx

Structural highlights

Function

References

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