2zj2: Difference between revisions

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==Archaeal DNA helicase Hjm apo state in form 1==
==Archaeal DNA helicase Hjm apo state in form 1==
<StructureSection load='2zj2' size='340' side='right' caption='[[2zj2]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
<StructureSection load='2zj2' size='340' side='right'caption='[[2zj2]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2zj2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZJ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZJ2 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2zj2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZJ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZJ2 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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]] 2.4&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2zj5|2zj5]], [[2zj8|2zj8]], [[2zja|2zja]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=2zj2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zj2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zj2 RCSB], [http://www.ebi.ac.uk/pdbsum/2zj2 PDBsum]</span></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=2zj2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zj2 OCA], [https://pdbe.org/2zj2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zj2 RCSB], [https://www.ebi.ac.uk/pdbsum/2zj2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zj2 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/HELS_PYRFU HELS_PYRFU]] DNA-dependent ATPase and 3'-5' DNA helicase that may be involved in repair of stalled replication forks. Unwinds the lagging strand from forked DNA structures in a 3'-5' direction. PCNA, the DNA polymerase sliding clamp subunit, stimulates the helicase activity, and may alter substrate specificity. Unwinds branched DNA (Holliday junctions) in an ATP-dependent fashion; ss- and dsDNA stimulate ATPase to the greatest extent, although it preferentially binds DNA with a single-stranded region. Processes a RecA-mediated recombination intermediate between gapped circular and homologus linear dsDNA.<ref>PMID:15677450</ref> <ref>PMID:16436047</ref>
[https://www.uniprot.org/uniprot/HELS_PYRFU HELS_PYRFU] DNA-dependent ATPase and 3'-5' DNA helicase that may be involved in repair of stalled replication forks. Unwinds the lagging strand from forked DNA structures in a 3'-5' direction. PCNA, the DNA polymerase sliding clamp subunit, stimulates the helicase activity, and may alter substrate specificity. Unwinds branched DNA (Holliday junctions) in an ATP-dependent fashion; ss- and dsDNA stimulate ATPase to the greatest extent, although it preferentially binds DNA with a single-stranded region. Processes a RecA-mediated recombination intermediate between gapped circular and homologus linear dsDNA.<ref>PMID:15677450</ref> <ref>PMID:16436047</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zj/2zj2_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zj/2zj2_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2zj2 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
BACKGROUND: Pyrococcus furiosus Hjm (PfuHjm) is a structure-specific DNA helicase that was originally identified by in vitro screening for Holliday junction migration activity. It belongs to helicase superfamily 2, and shares homology with the human DNA polymerase Theta (PolTheta), HEL308, and Drosophila Mus308 proteins, which are involved in DNA repair. Previous biochemical and genetic analyses revealed that PfuHjm preferentially binds to fork-related Y-structured DNAs and unwinds their double-stranded regions, suggesting that this helicase is a functional counterpart of the bacterial RecQ helicase, which is essential for genome maintenance. Elucidation of the DNA unwinding and translocation mechanisms by PfuHjm will require its three-dimensional structure at atomic resolution. RESULTS: We determined the crystal structures of PfuHjm, in two apo-states and two nucleotide bound forms, at resolutions of 2.0-2.7 A. The overall structures and the local conformations around the nucleotide binding sites are almost the same, including the side-chain conformations, irrespective of the nucleotide-binding states. The architecture of Hjm was similar to that of Archaeoglobus fulgidus Hel308 complexed with DNA. An Hjm-DNA complex model, constructed by fitting the five domains of Hjm onto the corresponding Hel308 domains, indicated that the interaction of Hjm with DNA is similar to that of Hel308. Notably, sulphate ions bound to Hjm lie on the putative DNA binding surfaces. Electron microscopic analysis of an Hjm-DNA complex revealed substantial flexibility of the double stranded region of DNA, presumably due to particularly weak protein-DNA interactions. Our present structures allowed reasonable homology model building of the helicase region of human PolTheta, indicating the strong conformational conservation between archaea and eukarya. CONCLUSION: The detailed comparison between our DNA-free PfuHjm structure and the structure of Hel308 complexed with DNA suggests similar DNA unwinding and translocation mechanisms, which could be generalized to all of the members in the same family. Structural comparison also implied a minor rearrangement of the five domains during DNA unwinding reaction. The unexpected small contact between the DNA duplex region and the enzyme appears to be advantageous for processive helicase activity.
Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm.,Oyama T, Oka H, Mayanagi K, Shirai T, Matoba K, Fujikane R, Ishino Y, Morikawa K BMC Struct Biol. 2009 Jan 22;9:2. PMID:19159486<ref>PMID:19159486</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrococcus furiosus]]
[[Category: Pyrococcus furiosus]]
[[Category: Fujikane, R]]
[[Category: Fujikane R]]
[[Category: Ishino, Y]]
[[Category: Ishino Y]]
[[Category: Morikawa, K]]
[[Category: Morikawa K]]
[[Category: Oka, H]]
[[Category: Oka H]]
[[Category: Oyama, T]]
[[Category: Oyama T]]
[[Category: Atp-binding]]
[[Category: Helicase]]
[[Category: Hydrolase]]
[[Category: Nucleotide-binding]]
[[Category: Reca fold]]

Latest revision as of 16:57, 13 March 2024

Archaeal DNA helicase Hjm apo state in form 1Archaeal DNA helicase Hjm apo state in form 1

Structural highlights

2zj2 is a 1 chain structure with sequence from Pyrococcus furiosus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HELS_PYRFU DNA-dependent ATPase and 3'-5' DNA helicase that may be involved in repair of stalled replication forks. Unwinds the lagging strand from forked DNA structures in a 3'-5' direction. PCNA, the DNA polymerase sliding clamp subunit, stimulates the helicase activity, and may alter substrate specificity. Unwinds branched DNA (Holliday junctions) in an ATP-dependent fashion; ss- and dsDNA stimulate ATPase to the greatest extent, although it preferentially binds DNA with a single-stranded region. Processes a RecA-mediated recombination intermediate between gapped circular and homologus linear dsDNA.[1] [2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ Fujikane R, Komori K, Shinagawa H, Ishino Y. Identification of a novel helicase activity unwinding branched DNAs from the hyperthermophilic archaeon, Pyrococcus furiosus. J Biol Chem. 2005 Apr 1;280(13):12351-8. Epub 2005 Jan 27. PMID:15677450 doi:http://dx.doi.org/10.1074/jbc.M413417200
  2. ↑ Fujikane R, Shinagawa H, Ishino Y. The archaeal Hjm helicase has recQ-like functions, and may be involved in repair of stalled replication fork. Genes Cells. 2006 Feb;11(2):99-110. PMID:16436047 doi:http://dx.doi.org/10.1111/j.1365-2443.2006.00925.x

2zj2, resolution 2.40Å

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