4nmn: Difference between revisions

Revision as of 08:34, 11 January 2023

Aquifex aeolicus replicative helicase (DnaB) complexed with ADP, at 3.3 resolution

Structural highlights

4nmn is a 2 chain structure with sequence from Aquifex aeolicus VF5. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	ADP, MG, SR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

O67450_AQUAE

Publication Abstract from PubMed

Cellular replication forks are powered by ring-shaped, hexameric helicases that encircle and unwind DNA. To better understand the molecular mechanisms and control of these enzymes, we used multiple methods to investigate the bacterial replicative helicase, DnaB. A 3.3 A crystal structure of Aquifex aeolicus DnaB, complexed with nucleotide, reveals a newly discovered conformational state for this motor protein. Electron microscopy and small angle X-ray scattering studies confirm the state seen crystallographically, showing that the DnaB ATPase domains and an associated N-terminal collar transition between two physical states in a nucleotide-dependent manner. Mutant helicases locked in either collar state are active but display different capacities to support critical activities such as duplex translocation and primase-dependent RNA synthesis. Our findings establish the DnaB collar as an autoregulatory hub that controls the ability of the helicase to transition between different functional states in response to both nucleotide and replication initiation/elongation factors.

Nucleotide and partner-protein control of bacterial replicative helicase structure and function.,Strycharska MS, Arias-Palomo E, Lyubimov AY, Erzberger JP, O'Shea VL, Bustamante CJ, Berger JM Mol Cell. 2013 Dec 26;52(6):844-54. doi: 10.1016/j.molcel.2013.11.016. PMID:24373746^[1]

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

References

↑ Strycharska MS, Arias-Palomo E, Lyubimov AY, Erzberger JP, O'Shea VL, Bustamante CJ, Berger JM. Nucleotide and partner-protein control of bacterial replicative helicase structure and function. Mol Cell. 2013 Dec 26;52(6):844-54. doi: 10.1016/j.molcel.2013.11.016. PMID:24373746 doi:https://dx.doi.org/10.1016/j.molcel.2013.11.016

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OCA

[1] Strycharska MS, Arias-Palomo E, Lyubimov AY, Erzberger JP, O'Shea VL, Bustamante CJ, Berger JM. Nucleotide and partner-protein control of bacterial replicative helicase structure and function. Mol Cell. 2013 Dec 26;52(6):844-54. doi: 10.1016/j.molcel.2013.11.016. PMID:24373746 doi:https://dx.doi.org/10.1016/j.molcel.2013.11.016

[1]

@@ Line 1: / Line 1: @@
 ==Aquifex aeolicus replicative helicase (DnaB) complexed with ADP, at 3.3 resolution==
-<StructureSection load='4nmn' size='340' side='right' caption='[[4nmn]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
+<StructureSection load='4nmn' size='340' side='right'caption='[[4nmn]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4nmn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquae Aquae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NMN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4nmn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NMN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NMN FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
+</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4esv|4esv]], [[2r6a|2r6a]]</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=4nmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nmn OCA], [https://pdbe.org/4nmn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nmn RCSB], [https://www.ebi.ac.uk/pdbsum/4nmn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nmn ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dnaB, aq_1472 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</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=4nmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nmn OCA], [http://pdbe.org/4nmn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nmn RCSB], [http://www.ebi.ac.uk/pdbsum/4nmn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nmn ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/O67450_AQUAE O67450_AQUAE]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Aquae]]
+[[Category: Aquifex aeolicus VF5]]
-[[Category: Berger, J M]]
+[[Category: Large Structures]]
-[[Category: Erzberger, J P]]
+[[Category: Berger JM]]
-[[Category: Lyubimov, A Y]]
+[[Category: Erzberger JP]]
-[[Category: Strycharska, M S]]
+[[Category: Lyubimov AY]]
-[[Category: Atp binding]]
+[[Category: Strycharska MS]]
-[[Category: Dna-binding]]
-[[Category: Reca-type helicase]]
-[[Category: Replication]]
-[[Category: Replicative dna helicase]]

4nmn: Difference between revisions

Revision as of 08:34, 11 January 2023

Aquifex aeolicus replicative helicase (DnaB) complexed with ADP, at 3.3 resolution

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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