6qem: Difference between revisions

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~~'''Unreleased structure'''~~

~~The entry~~ 6qem is ~~ON HOLD~~

==E. coli DnaBC complex bound to ssDNA==

== Structural highlights ==

<table><tr><td colspan='2'>[[6qem]] is a 13 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QEM FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.4Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=08T:[[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]OXY-TRIS(FLUORANYL)BERYLLIUM'>08T</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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=6qem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qem OCA], [https://pdbe.org/6qem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qem RCSB], [https://www.ebi.ac.uk/pdbsum/6qem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qem ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/DNAB_ECOLI DNAB_ECOLI] Participates in initiation and elongation during chromosome replication; it exhibits DNA-dependent ATPase activity and contains distinct active sites for ATP binding, DNA binding, and interaction with DnaC protein, primase, and other prepriming proteins.

== Publication Abstract from PubMed ==

In cells, dedicated AAA+ ATPases deposit hexameric, ring-shaped helicases onto DNA to initiate chromosomal replication. To better understand the mechanisms by which helicase loading can occur, we used cryo-EM to determine sub-4-A-resolution structures of the E. coli DnaBDnaC helicaseloader complex with nucleotide in pre- and post-DNA engagement states. In the absence of DNA, six DnaC protomers latch onto and crack open a DnaB hexamer using an extended N-terminal domain, stabilizing this conformation through nucleotide-dependent ATPase interactions. Upon binding DNA, DnaC hydrolyzes ATP, allowing DnaB to isomerize into a topologically closed, pre-translocation state competent to bind primase. Our data show how DnaC opens the DnaB ring and represses the helicase prior to DNA binding and how DnaC ATPase activity is reciprocally regulated by DnaB and DNA. Comparative analyses reveal how the helicase loading mechanism of DnaC parallels and diverges from homologous AAA+ systems involved in DNA replication and transposition.

~~Authors~~:

Physical Basis for the Loading of a Bacterial Replicative Helicase onto DNA.,Arias-Palomo E, Puri N, O'Shea Murray VL, Yan Q, Berger JM Mol Cell. 2019 Feb 16. pii: S1097-2765(19)30043-7. doi:, 10.1016/j.molcel.2019.01.023. PMID:30797687<ref>PMID:30797687</ref>

~~Description~~:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

==See Also==

*[[DnaC helicase loader|DnaC helicase loader]]

*[[Helicase 3D structures|Helicase 3D structures]]

== References ==

__TOC__

</SX>

[[Category: Escherichia coli]]

[[Category: Large Structures]]

[[Category: Arias-Palomo E]]

[[Category: Berger JM]]

[[Category: O'Shea Murray VL]]

[[Category: Puri N]]

[[Category: Yan Q]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6qem is ON HOLD
+==E. coli DnaBC complex bound to ssDNA==
+<SX load='6qem' size='340' side='right' viewer='molstar' caption='[[6qem]], [[Resolution|resolution]] 3.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6qem]] is a 13 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QEM FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.4&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=08T:[[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]OXY-TRIS(FLUORANYL)BERYLLIUM'>08T</scene>, <scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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=6qem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qem OCA], [https://pdbe.org/6qem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qem RCSB], [https://www.ebi.ac.uk/pdbsum/6qem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qem ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DNAB_ECOLI DNAB_ECOLI] Participates in initiation and elongation during chromosome replication; it exhibits DNA-dependent ATPase activity and contains distinct active sites for ATP binding, DNA binding, and interaction with DnaC protein, primase, and other prepriming proteins.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In cells, dedicated AAA+ ATPases deposit hexameric, ring-shaped helicases onto DNA to initiate chromosomal replication. To better understand the mechanisms by which helicase loading can occur, we used cryo-EM to determine sub-4-A-resolution structures of the E. coli DnaBDnaC helicaseloader complex with nucleotide in pre- and post-DNA engagement states. In the absence of DNA, six DnaC protomers latch onto and crack open a DnaB hexamer using an extended N-terminal domain, stabilizing this conformation through nucleotide-dependent ATPase interactions. Upon binding DNA, DnaC hydrolyzes ATP, allowing DnaB to isomerize into a topologically closed, pre-translocation state competent to bind primase. Our data show how DnaC opens the DnaB ring and represses the helicase prior to DNA binding and how DnaC ATPase activity is reciprocally regulated by DnaB and DNA. Comparative analyses reveal how the helicase loading mechanism of DnaC parallels and diverges from homologous AAA+ systems involved in DNA replication and transposition.
-Authors:
+Physical Basis for the Loading of a Bacterial Replicative Helicase onto DNA.,Arias-Palomo E, Puri N, O'Shea Murray VL, Yan Q, Berger JM Mol Cell. 2019 Feb 16. pii: S1097-2765(19)30043-7. doi:, 10.1016/j.molcel.2019.01.023. PMID:30797687<ref>PMID:30797687</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6qem" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[DnaC helicase loader|DnaC helicase loader]]
+*[[Helicase 3D structures|Helicase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</SX>
+[[Category: Escherichia coli]]
+[[Category: Large Structures]]
+[[Category: Arias-Palomo E]]
+[[Category: Berger JM]]
+[[Category: O'Shea Murray VL]]
+[[Category: Puri N]]
+[[Category: Yan Q]]