2cvf: Difference between revisions

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[[Image:2cvf.gif|left|200px]]


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==Crystal structure of the RadB recombinase==
The line below this paragraph, containing "STRUCTURE_2cvf", creates the "Structure Box" on the page.
<StructureSection load='2cvf' size='340' side='right'caption='[[2cvf]], [[Resolution|resolution]] 2.60&Aring;' 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'>[[2cvf]] 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=2CVF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CVF 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]] 2.6&#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=2cvf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cvf OCA], [https://pdbe.org/2cvf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cvf RCSB], [https://www.ebi.ac.uk/pdbsum/2cvf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cvf ProSAT]</span></td></tr>
{{STRUCTURE_2cvf| PDB=2cvf |  SCENE= }}
</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/2cvf_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=2cvf ConSurf].
<div style="clear:both"></div>


'''Crystal structure of the RadB recombinase'''
==See Also==
 
*[[Resolvase 3D structures|Resolvase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
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.
[[Category: Large Structures]]
 
==About this Structure==
2CVF is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CVF OCA].
 
==Reference==
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:[http://www.ncbi.nlm.nih.gov/pubmed/15956102 15956102]
[[Category: Single protein]]
[[Category: Thermococcus kodakarensis]]
[[Category: Thermococcus kodakarensis]]
[[Category: Akiba, T.]]
[[Category: Akiba T]]
[[Category: Harata, K.]]
[[Category: Harata K]]
[[Category: Imanaka, T.]]
[[Category: Imanaka T]]
[[Category: Ishii, N.]]
[[Category: Ishii N]]
[[Category: Morikawa, M.]]
[[Category: Morikawa M]]
[[Category: Rashid, N.]]
[[Category: Rashid N]]
[[Category: Atpase domain]]
[[Category: Filament formation]]
[[Category: Homologous recombination]]
[[Category: Hyperthermophile]]
[[Category: Radb]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 23:09:06 2008''

Latest revision as of 16:43, 13 March 2024

Crystal structure of the RadB recombinaseCrystal structure of the RadB recombinase

Structural highlights

2cvf is a 2 chain structure with sequence from Thermococcus kodakarensis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.6Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

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

See Also

2cvf, resolution 2.60Å

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