1gef: Difference between revisions
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< | ==Crystal structure of the archaeal holliday junction resolvase HJC== | ||
<StructureSection load='1gef' size='340' side='right'caption='[[1gef]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
You may | == Structural highlights == | ||
<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> | |||
</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> | |||
<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 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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1gef" style="background-color:#fffaf0;"></div> | |||
== | |||
==See Also== | ==See Also== | ||
*[[Resolvase]] | *[[Resolvase 3D structures|Resolvase 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Pyrococcus furiosus]] | [[Category: Pyrococcus furiosus]] | ||
[[Category: Ishino | [[Category: Ishino Y]] | ||
[[Category: Komori | [[Category: Komori K]] | ||
[[Category: Morikawa | [[Category: Morikawa K]] | ||
[[Category: Nishino | [[Category: Nishino T]] | ||
[[Category: Tsuchiya | [[Category: Tsuchiya D]] | ||