1ipi: Difference between revisions

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[[Image:1ipi.png|left|200px]]


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==CRYSTAL STRUCTURE OF THE ARCHAEAL HOLLIDAY JUNCTION RESOLVASE HJC FROM PYROCOCCUS FURIOSUS FORM II==
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<StructureSection load='1ipi' size='340' side='right'caption='[[1ipi]], [[Resolution|resolution]] 2.16&Aring;' scene=''>
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== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1ipi]] is a 2 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=1IPI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IPI FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.16&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ipi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ipi OCA], [https://pdbe.org/1ipi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ipi RCSB], [https://www.ebi.ac.uk/pdbsum/1ipi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ipi ProSAT]</span></td></tr>
{{STRUCTURE_1ipi|  PDB=1ipi  |  SCENE=  }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/HJC_PYRFU HJC_PYRFU] A structure-specific endonuclease that resolves Holliday junction (HJ) intermediates during genetic recombination. Cleaves 4-way DNA junctions introducing paired nicks in opposing strands, leaving a 5'-terminal phosphate and a 3'-terminal hydroxyl group that are ligated to produce recombinant products. Cleaves both mobile and immobile junctions. Binds 4-way junction DNA, a synthetic Hj, binding is not competed by dsDNA.[HAMAP-Rule:MF_01490]<ref>PMID:10430863</ref> <ref>PMID:11005813</ref> <ref>PMID:11071944</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ip/1ipi_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </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/main_output.php?pdb_ID=1ipi ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Hjc is an archaeal DNA endonuclease, which resolves the Holliday junction in the presence of divalent metals. Combined with mutational analyses, the x-ray structure of the Pyrococcus furiosus Hjc crystal grown in the presence of ammonium sulfate revealed a positively charged interface, rich in conserved basic residues, and the catalytic center (Nishino, T., Komori, K., Tsuchiya, D., Ishino, Y., and Morikawa, K. (2001) Structure 9, 197-T204). This structural study also suggested that the N-terminal segment and some loops of Hjc play crucial roles in the cleavage of DNA. However, a structural view of the interaction between these regions and DNA remains elusive. To clarify the regional roles of Hjc in the recognition of the Holliday junction, further structural and biochemical analyses were carried out. A new crystal form of Hjc was obtained from a polyethylene glycol solution in the absence of ammonium sulfate, and its structure has been determined at 2.16-A resolution. A comparison of the two crystal structures has revealed that the N-terminal segment undergoes a serious conformational change. The site-directed mutagenesis of the sulfate-binding site within the segment caused a dramatic decrease in the junction binding, but the mutant was still capable of cleaving DNA with a 20-fold lower efficiency. The kinetic analysis of Hjc-Holliday junction interaction indicated that mutations in the N-terminal segment greatly increased the dissociation rate constants of the Hjc-Holliday junction complex, explaining the decreased stability of the complex. This segment is also responsible for the disruption of base pairs near the junction center, through specific interactions with them. Taken together, these results imply that, in addition to the secondary effects of two basic loops, the flexible N-terminal segment plays predominant roles in the recognition of DNA conformation near the crossover and in correct positioning of the cleavage site to the catalytic center of the Hjc resolvase.


===CRYSTAL STRUCTURE OF THE ARCHAEAL HOLLIDAY JUNCTION RESOLVASE HJC FROM PYROCOCCUS FURIOSUS FORM II===
Dissection of the regional roles of the archaeal Holliday junction resolvase Hjc by structural and mutational analyses.,Nishino T, Komori K, Ishino Y, Morikawa K J Biol Chem. 2001 Sep 21;276(38):35735-40. Epub 2001 Jul 5. PMID:11441015<ref>PMID:11441015</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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{{ABSTRACT_PUBMED_11441015}}
 
==About this Structure==
[[1ipi]] is a 2 chain structure of [[Resolvase]] 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=1IPI OCA].


==See Also==
==See Also==
*[[Resolvase]]
*[[Resolvase 3D structures|Resolvase 3D structures]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:11441015</ref><references group="xtra"/>
__TOC__
[[Category: Crossover junction endodeoxyribonuclease]]
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrococcus furiosus]]
[[Category: Pyrococcus furiosus]]
[[Category: Ishino, Y.]]
[[Category: Ishino Y]]
[[Category: Komori, K.]]
[[Category: Komori K]]
[[Category: Morikawa, K.]]
[[Category: Morikawa K]]
[[Category: Nishino, T.]]
[[Category: Nishino T]]
[[Category: Hjc]]
[[Category: Hydrolase]]
[[Category: Nuclease fold]]

Latest revision as of 10:11, 25 October 2023

CRYSTAL STRUCTURE OF THE ARCHAEAL HOLLIDAY JUNCTION RESOLVASE HJC FROM PYROCOCCUS FURIOSUS FORM IICRYSTAL STRUCTURE OF THE ARCHAEAL HOLLIDAY JUNCTION RESOLVASE HJC FROM PYROCOCCUS FURIOSUS FORM II

Structural highlights

1ipi is a 2 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 2.16Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HJC_PYRFU A structure-specific endonuclease that resolves Holliday junction (HJ) intermediates during genetic recombination. Cleaves 4-way DNA junctions introducing paired nicks in opposing strands, leaving a 5'-terminal phosphate and a 3'-terminal hydroxyl group that are ligated to produce recombinant products. Cleaves both mobile and immobile junctions. Binds 4-way junction DNA, a synthetic Hj, binding is not competed by dsDNA.[HAMAP-Rule:MF_01490][1] [2] [3]

Evolutionary Conservation

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

Publication Abstract from PubMed

Hjc is an archaeal DNA endonuclease, which resolves the Holliday junction in the presence of divalent metals. Combined with mutational analyses, the x-ray structure of the Pyrococcus furiosus Hjc crystal grown in the presence of ammonium sulfate revealed a positively charged interface, rich in conserved basic residues, and the catalytic center (Nishino, T., Komori, K., Tsuchiya, D., Ishino, Y., and Morikawa, K. (2001) Structure 9, 197-T204). This structural study also suggested that the N-terminal segment and some loops of Hjc play crucial roles in the cleavage of DNA. However, a structural view of the interaction between these regions and DNA remains elusive. To clarify the regional roles of Hjc in the recognition of the Holliday junction, further structural and biochemical analyses were carried out. A new crystal form of Hjc was obtained from a polyethylene glycol solution in the absence of ammonium sulfate, and its structure has been determined at 2.16-A resolution. A comparison of the two crystal structures has revealed that the N-terminal segment undergoes a serious conformational change. The site-directed mutagenesis of the sulfate-binding site within the segment caused a dramatic decrease in the junction binding, but the mutant was still capable of cleaving DNA with a 20-fold lower efficiency. The kinetic analysis of Hjc-Holliday junction interaction indicated that mutations in the N-terminal segment greatly increased the dissociation rate constants of the Hjc-Holliday junction complex, explaining the decreased stability of the complex. This segment is also responsible for the disruption of base pairs near the junction center, through specific interactions with them. Taken together, these results imply that, in addition to the secondary effects of two basic loops, the flexible N-terminal segment plays predominant roles in the recognition of DNA conformation near the crossover and in correct positioning of the cleavage site to the catalytic center of the Hjc resolvase.

Dissection of the regional roles of the archaeal Holliday junction resolvase Hjc by structural and mutational analyses.,Nishino T, Komori K, Ishino Y, Morikawa K J Biol Chem. 2001 Sep 21;276(38):35735-40. Epub 2001 Jul 5. PMID:11441015[4]

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

See Also

References

  1. ↑ Komori K, Sakae S, Shinagawa H, Morikawa K, Ishino Y. A Holliday junction resolvase from Pyrococcus furiosus: functional similarity to Escherichia coli RuvC provides evidence for conserved mechanism of homologous recombination in Bacteria, Eukarya, and Archaea. Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):8873-8. PMID:10430863
  2. ↑ Komori K, Sakae S, Daiyasu H, Toh H, Morikawa K, Shinagawa H, Ishino Y. Mutational analysis of the Pyrococcus furiosus holliday junction resolvase hjc revealed functionally important residues for dimer formation, junction DNA binding, and cleavage activities. J Biol Chem. 2000 Dec 22;275(51):40385-91. PMID:11005813 doi:http://dx.doi.org/10.1074/jbc.M006294200
  3. ↑ Komori K, Sakae S, Fujikane R, Morikawa K, Shinagawa H, Ishino Y. Biochemical characterization of the hjc holliday junction resolvase of Pyrococcus furiosus. Nucleic Acids Res. 2000 Nov 15;28(22):4544-51. PMID:11071944
  4. ↑ Nishino T, Komori K, Ishino Y, Morikawa K. Dissection of the regional roles of the archaeal Holliday junction resolvase Hjc by structural and mutational analyses. J Biol Chem. 2001 Sep 21;276(38):35735-40. Epub 2001 Jul 5. PMID:11441015 doi:10.1074/jbc.M104460200

1ipi, resolution 2.16Å

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