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3bm3

From Proteopedia

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(New page: 200px <!-- The line below this paragraph, containing "STRUCTURE_3bm3", creates the "Structure Box" on the page. You may change the PDB parameter (which sets the PD...)
Current revision (18:58, 20 October 2021) (edit) (undo)
 
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[[Image:3bm3.png|left|200px]]
 
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==Restriction endonuclease PspGI-substrate DNA complex==
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The line below this paragraph, containing "STRUCTURE_3bm3", creates the "Structure Box" on the page.
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<StructureSection load='3bm3' size='340' side='right'caption='[[3bm3]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3bm3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_sp._gi-h Pyrococcus sp. gi-h]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BM3 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene></td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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{{STRUCTURE_3bm3| PDB=3bm3 | SCENE= }}
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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=3bm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm3 OCA], [https://pdbe.org/3bm3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bm3 RCSB], [https://www.ebi.ac.uk/pdbsum/3bm3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bm3 ProSAT]</span></td></tr>
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</table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bm/3bm3_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3bm3 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Many DNA modification and repair enzymes require access to DNA bases and therefore flip nucleotides. Restriction endonucleases (REases) hydrolyze the phosphodiester backbone within or in the vicinity of the target recognition site and do not require base extrusion for the sequence readout and catalysis. Therefore, the observation of extrahelical nucleotides in a co-crystal of REase Ecl18kI with the cognate sequence, CCNGG, was unexpected. It turned out that Ecl18kI reads directly only the CCGG sequence and skips the unspecified N nucleotides, flipping them out from the helix. Sequence and structure conservation predict nucleotide flipping also for the complexes of PspGI and EcoRII with their target DNAs (/CCWGG), but data in solution are limited and indirect. Here, we demonstrate that Ecl18kI, the C-terminal domain of EcoRII (EcoRII-C) and PspGI enhance the fluorescence of 2-aminopurines (2-AP) placed at the centers of their recognition sequences. The fluorescence increase is largest for PspGI, intermediate for EcoRII-C and smallest for Ecl18kI, probably reflecting the differences in the hydrophobicity of the binding pockets within the protein. Omitting divalent metal cations and mutation of the binding pocket tryptophan to alanine strongly increase the 2-AP signal in the Ecl18kI-DNA complex. Together, our data provide the first direct evidence that Ecl18kI, EcoRII-C and PspGI flip nucleotides in solution.
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===Restriction endonuclease PspGI-substrate DNA complex===
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Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence.,Tamulaitis G, Zaremba M, Szczepanowski RH, Bochtler M, Siksnys V Nucleic Acids Res. 2007;35(14):4792-9. Epub 2007 Jul 7. PMID:17617640<ref>PMID:17617640</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_17617640}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3bm3" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 17617640 is the PubMed ID number.
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{{ABSTRACT_PUBMED_17617640}}
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==About this Structure==
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[[3bm3]] is a 4 chain structure of [[Endonuclease]] with sequence from [http://en.wikipedia.org/wiki/Archaea Archaea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM3 OCA].
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==See Also==
==See Also==
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*[[Endonuclease|Endonuclease]]
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:017617640</ref><ref group="xtra">PMID:016893959</ref><ref group="xtra">PMID:012798682</ref><ref group="xtra">PMID:009758783</ref><references group="xtra"/>
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__TOC__
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[[Category: Archaea]]
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</StructureSection>
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[[Category: Bhagwat, A.]]
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[[Category: Large Structures]]
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[[Category: Bochtler, M.]]
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[[Category: Pyrococcus sp. gi-h]]
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[[Category: Carpenter, M.]]
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[[Category: Bhagwat, A]]
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[[Category: Czapinska, H.]]
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[[Category: Bochtler, M]]
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[[Category: Siksnys, V.]]
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[[Category: Carpenter, M]]
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[[Category: Szczepanowski, R H.]]
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[[Category: Czapinska, H]]
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[[Category: Tamulaitis, G.]]
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[[Category: Siksnys, V]]
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[[Category: Szczepanowski, R H]]
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[[Category: Tamulaitis, G]]
[[Category: Base flipping]]
[[Category: Base flipping]]
[[Category: Endonuclease-dna complex]]
[[Category: Endonuclease-dna complex]]

Current revision

Restriction endonuclease PspGI-substrate DNA complex

PDB ID 3bm3

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