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| - | [[Image:1gef.gif|left|200px]] | |
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| - | <!-- | + | ==Crystal structure of the archaeal holliday junction resolvase HJC== |
| - | The line below this paragraph, containing "STRUCTURE_1gef", creates the "Structure Box" on the page.
| + | <StructureSection load='1gef' size='340' side='right'caption='[[1gef]], [[Resolution|resolution]] 2.00Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet) | + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[1gef]] is a 4 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=1GEF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GEF FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</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> |
| - | {{STRUCTURE_1gef| PDB=1gef | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gef OCA], [https://pdbe.org/1gef PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gef RCSB], [https://www.ebi.ac.uk/pdbsum/1gef PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gef ProSAT]</span></td></tr> |
| | + | </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/ge/1gef_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=1gef ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | BACKGROUND: Homologous recombination is a crucial mechanism in determining genetic diversity and repairing damaged chromosomes. Holliday junction is the universal DNA intermediate whose interaction with proteins is one of the major events in the recombinational process. Hjc is an archaeal endonuclease, which specifically resolves the junction DNA to produce two separate recombinant DNA duplexes. The atomic structure of Hjc should clarify the mechanisms of the specific recognition with Holliday junction and the catalytic reaction. RESULTS: The crystal structure of Hjc from the hyperthermophilic archaeon Pyrococcus furiosus has been determined at 2.0 A resolution. The active Hjc molecule forms a homodimer, where an extensive hydrophobic interface tightly assembles two subunits of a single compact domain. The folding of the Hjc subunit is clearly different from any other Holliday junction resolvases thus far known. Instead, it resembles those of type II restriction endonucleases, including the configurations of the active site residues, which constitute the canonical catalytic motifs. The dimeric Hjc molecule displays an extensive basic surface on one side, which contains many conserved amino acids, including those in the active site. CONCLUSIONS: The architectural similarity of Hjc to restriction endonucleases allowed us to construct a putative model of the complex with Holliday junction. This model accounts for how Hjc recognizes and resolves the junction DNA in a specific manner. Mutational and biochemical analyses highlight the importance of some loops and the amino terminal region in interaction with DNA. |
| | | | |
| - | '''CRYSTAL STRUCTURE OF THE ARCHAEAL HOLLIDAY JUNCTION RESOLVASE HJC'''
| + | Crystal structure of the archaeal holliday junction resolvase Hjc and implications for DNA recognition.,Nishino T, Komori K, Tsuchiya D, Ishino Y, Morikawa K Structure. 2001 Mar 7;9(3):197-204. PMID:11286886<ref>PMID:11286886</ref> |
| - | | + | |
| - | | + | |
| - | ==Overview==
| + | |
| - | BACKGROUND: Homologous recombination is a crucial mechanism in determining genetic diversity and repairing damaged chromosomes. Holliday junction is the universal DNA intermediate whose interaction with proteins is one of the major events in the recombinational process. Hjc is an archaeal endonuclease, which specifically resolves the junction DNA to produce two separate recombinant DNA duplexes. The atomic structure of Hjc should clarify the mechanisms of the specific recognition with Holliday junction and the catalytic reaction. RESULTS: The crystal structure of Hjc from the hyperthermophilic archaeon Pyrococcus furiosus has been determined at 2.0 A resolution. The active Hjc molecule forms a homodimer, where an extensive hydrophobic interface tightly assembles two subunits of a single compact domain. The folding of the Hjc subunit is clearly different from any other Holliday junction resolvases thus far known. Instead, it resembles those of type II restriction endonucleases, including the configurations of the active site residues, which constitute the canonical catalytic motifs. The dimeric Hjc molecule displays an extensive basic surface on one side, which contains many conserved amino acids, including those in the active site. CONCLUSIONS: The architectural similarity of Hjc to restriction endonucleases allowed us to construct a putative model of the complex with Holliday junction. This model accounts for how Hjc recognizes and resolves the junction DNA in a specific manner. Mutational and biochemical analyses highlight the importance of some loops and the amino terminal region in interaction with DNA.
| + | |
| | | | |
| - | ==About this Structure==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | 1GEF is a [[Single protein]] structure of 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=1GEF OCA].
| + | </div> |
| | + | <div class="pdbe-citations 1gef" style="background-color:#fffaf0;"></div> |
| | | | |
| - | ==Reference== | + | ==See Also== |
| - | Crystal structure of the archaeal holliday junction resolvase Hjc and implications for DNA recognition., Nishino T, Komori K, Tsuchiya D, Ishino Y, Morikawa K, Structure. 2001 Mar 7;9(3):197-204. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11286886 11286886]
| + | *[[Resolvase 3D structures|Resolvase 3D structures]] |
| | + | == References == |
| | + | <references/> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Pyrococcus furiosus]] | | [[Category: Pyrococcus furiosus]] |
| - | [[Category: Single protein]]
| + | [[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: Tsuchiya D]] |
| - | [[Category: Tsuchiya, D.]] | + | |
| - | [[Category: Hjc]]
| + | |
| - | [[Category: Holliday junction resolvase]]
| + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 17:28:16 2008''
| + | |
| 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
BACKGROUND: Homologous recombination is a crucial mechanism in determining genetic diversity and repairing damaged chromosomes. Holliday junction is the universal DNA intermediate whose interaction with proteins is one of the major events in the recombinational process. Hjc is an archaeal endonuclease, which specifically resolves the junction DNA to produce two separate recombinant DNA duplexes. The atomic structure of Hjc should clarify the mechanisms of the specific recognition with Holliday junction and the catalytic reaction. RESULTS: The crystal structure of Hjc from the hyperthermophilic archaeon Pyrococcus furiosus has been determined at 2.0 A resolution. The active Hjc molecule forms a homodimer, where an extensive hydrophobic interface tightly assembles two subunits of a single compact domain. The folding of the Hjc subunit is clearly different from any other Holliday junction resolvases thus far known. Instead, it resembles those of type II restriction endonucleases, including the configurations of the active site residues, which constitute the canonical catalytic motifs. The dimeric Hjc molecule displays an extensive basic surface on one side, which contains many conserved amino acids, including those in the active site. CONCLUSIONS: The architectural similarity of Hjc to restriction endonucleases allowed us to construct a putative model of the complex with Holliday junction. This model accounts for how Hjc recognizes and resolves the junction DNA in a specific manner. Mutational and biochemical analyses highlight the importance of some loops and the amino terminal region in interaction with DNA.
Crystal structure of the archaeal holliday junction resolvase Hjc and implications for DNA recognition.,Nishino T, Komori K, Tsuchiya D, Ishino Y, Morikawa K Structure. 2001 Mar 7;9(3):197-204. PMID:11286886[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, Tsuchiya D, Ishino Y, Morikawa K. Crystal structure of the archaeal holliday junction resolvase Hjc and implications for DNA recognition. Structure. 2001 Mar 7;9(3):197-204. PMID:11286886
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