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| | ==CRYSTAL STRUCTURE OF THE ARCHAEAL HOLLIDAY JUNCTION RESOLVASE HJC FROM PYROCOCCUS FURIOSUS FORM II== | | ==CRYSTAL STRUCTURE OF THE ARCHAEAL HOLLIDAY JUNCTION RESOLVASE HJC FROM PYROCOCCUS FURIOSUS FORM II== |
| - | <StructureSection load='1ipi' size='340' side='right' caption='[[1ipi]], [[Resolution|resolution]] 2.16Å' scene=''> | + | <StructureSection load='1ipi' size='340' side='right'caption='[[1ipi]], [[Resolution|resolution]] 2.16Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1ipi]] is a 2 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=1IPI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IPI FirstGlance]. <br> | + | <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> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1gef|1gef]]</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]] 2.16Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HJC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 Pyrococcus furiosus])</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=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> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Crossover_junction_endodeoxyribonuclease Crossover junction endodeoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.22.4 3.1.22.4] </span></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=1ipi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ipi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ipi RCSB], [http://www.ebi.ac.uk/pdbsum/1ipi PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Q9V301_PYRFU Q9V301_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.<ref>PMID:10430863</ref> <ref>PMID:11005813</ref> <ref>PMID:11071944</ref> | + | [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 == | | == 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/ip/1ipi_consurf.spt"</scriptWhenChecked> | + | <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> | | <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=1ipi ConSurf]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 1ipi" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Resolvase|Resolvase]] | + | *[[Resolvase 3D structures|Resolvase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Crossover junction endodeoxyribonuclease]] | + | [[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]]
| + | |
| Structural highlights
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
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
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