2cvh: Difference between revisions
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< | ==Crystal structure of the RadB recombinase== | ||
<StructureSection load='2cvh' size='340' side='right'caption='[[2cvh]], [[Resolution|resolution]] 2.20Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2cvh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CVH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CVH 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]] 2.2Å</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=2cvh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cvh OCA], [https://pdbe.org/2cvh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cvh RCSB], [https://www.ebi.ac.uk/pdbsum/2cvh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cvh ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/RADB_THEKO RADB_THEKO] Involved in DNA repair and in homologous recombination. May regulate the cleavage reactions of the branch-structured DNA. Has a very weak ATPase activity that is not stimulated by DNA. Binds DNA but does not promote DNA strands exchange (By similarity). | |||
== 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/cv/2cvh_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=2cvh ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The X-ray crystal structure of RadB from Thermococcus kodakaraensis KOD1, an archaeal homologue of the RecA/Rad51 family proteins, have been determined in two crystal forms. The structure represents the core ATPase domain of the RecA/Rad51 proteins. Two independent molecules in the type 1 crystal were roughly related by 7-fold screw symmetry whereas non-crystallographic 2-fold symmetry was observed in the type 2 crystal. The dimer structure in the type 1 crystal is extended to construct a helical assembly, which resembles the filamentous structures reported for other RecA/Rad51 proteins. The molecular interface in the type 1 dimer is formed by facing a basic surface patch of one monomer to an acidic one of the other. The empty ATP binding pocket is located at the interface and barely concealed from the outside similarly to that in the active form of the RecA filament. The model assembly has a positively charged belt on one surface bordering the helical groove suitable for facile binding of DNA. Electron microscopy has revealed that, in the absence of ATP and DNA, RadB forms a filament with a similar diameter to that of the hypothetical assembly, although its helical properties were not confirmed. | |||
Structure of RadB recombinase from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1: an implication for the formation of a near-7-fold helical assembly.,Akiba T, Ishii N, Rashid N, Morikawa M, Imanaka T, Harata K Nucleic Acids Res. 2005 Jun 13;33(10):3412-23. Print 2005. PMID:15956102<ref>PMID:15956102</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2cvh" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Resolvase 3D structures|Resolvase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
== | |||
[[Category: | |||
[[Category: Thermococcus kodakarensis]] | [[Category: Thermococcus kodakarensis]] | ||
[[Category: Akiba | [[Category: Akiba T]] | ||
[[Category: Harata | [[Category: Harata K]] | ||
[[Category: Imanaka | [[Category: Imanaka T]] | ||
[[Category: Ishii | [[Category: Ishii N]] | ||
[[Category: Morikawa | [[Category: Morikawa M]] | ||
[[Category: Rashid | [[Category: Rashid N]] | ||
Latest revision as of 11:20, 25 October 2023
Crystal structure of the RadB recombinaseCrystal structure of the RadB recombinase
Structural highlights
FunctionRADB_THEKO Involved in DNA repair and in homologous recombination. May regulate the cleavage reactions of the branch-structured DNA. Has a very weak ATPase activity that is not stimulated by DNA. Binds DNA but does not promote DNA strands exchange (By similarity). 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 PubMedThe X-ray crystal structure of RadB from Thermococcus kodakaraensis KOD1, an archaeal homologue of the RecA/Rad51 family proteins, have been determined in two crystal forms. The structure represents the core ATPase domain of the RecA/Rad51 proteins. Two independent molecules in the type 1 crystal were roughly related by 7-fold screw symmetry whereas non-crystallographic 2-fold symmetry was observed in the type 2 crystal. The dimer structure in the type 1 crystal is extended to construct a helical assembly, which resembles the filamentous structures reported for other RecA/Rad51 proteins. The molecular interface in the type 1 dimer is formed by facing a basic surface patch of one monomer to an acidic one of the other. The empty ATP binding pocket is located at the interface and barely concealed from the outside similarly to that in the active form of the RecA filament. The model assembly has a positively charged belt on one surface bordering the helical groove suitable for facile binding of DNA. Electron microscopy has revealed that, in the absence of ATP and DNA, RadB forms a filament with a similar diameter to that of the hypothetical assembly, although its helical properties were not confirmed. Structure of RadB recombinase from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1: an implication for the formation of a near-7-fold helical assembly.,Akiba T, Ishii N, Rashid N, Morikawa M, Imanaka T, Harata K Nucleic Acids Res. 2005 Jun 13;33(10):3412-23. Print 2005. PMID:15956102[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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