3bm3: Difference between revisions

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-[[Image:3bm3.png|left|200px]]
-<!--
+==Restriction endonuclease PspGI-substrate DNA complex==
-The line below this paragraph, containing "STRUCTURE_3bm3", creates the "Structure Box" on the page.
+<StructureSection load='3bm3' size='340' side='right'caption='[[3bm3]], [[Resolution|resolution]] 1.70&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'>[[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>
-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]] 1.7&#8491;</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>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_3bm3|  PDB=3bm3  |  SCENE=  }}
+<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>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/O93646_9EURY O93646_9EURY]
+== 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/bm/3bm3_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3bm3 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+An extremely thermostable restriction endonuclease, PspGI, was purified from Pyrococcus sp. strain GI-H. PspGI is an isoschizomer of EcoRII and cleaves DNA before the first C in the sequence 5' CCWGG 3' (W is A or T). PspGI digestion can be carried out at 65 to 85 degrees C. To express PspGI at high levels, the PspGI restriction-modification genes (pspGIR and pspGIM) were cloned in Escherichia coli. M.PspGI contains the conserved sequence motifs of alpha-aminomethyltransferases; therefore, it must be an N4-cytosine methylase. M.PspGI shows 53% similarity to (44% identity with) its isoschizomer, M.MvaI from Micrococcus variabilis. In a segment of 87 amino acid residues, PspGI shows significant sequence similarity to EcoRII and to regions of SsoII and StyD4I which have a closely related recognition sequence (5' CCNGG 3'). PspGI was expressed in E. coli via a T7 expression system. Recombinant PspGI was purified to near homogeneity and had a half-life of 2 h at 95 degrees C. PspGI remained active following 30 cycles of thermocycling; thus, it can be used in DNA-based diagnostic applications.
-===Restriction endonuclease PspGI-substrate DNA complex===
+Characterization of an extremely thermostable restriction enzyme, PspGI, from a Pyrococcus strain and cloning of the PspGI restriction-modification system in Escherichia coli.,Morgan R, Xiao J, Xu S Appl Environ Microbiol. 1998 Oct;64(10):3669-73. PMID:009758783<ref>PMID:009758783</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_17617640}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3bm3" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17617640 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_17617640}}
-==About this Structure==
-[[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].
 ==See Also==
-*[[Endonuclease|Endonuclease]]
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
+== References ==
-==Reference==
+<references/>
-<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"/>
+__TOC__
-[[Category: Archaea]]
+</StructureSection>
-[[Category: Bhagwat, A.]]
+[[Category: Large Structures]]
-[[Category: Bochtler, M.]]
+[[Category: Pyrococcus sp. GI-H]]
-[[Category: Carpenter, M.]]
+[[Category: Bhagwat A]]
-[[Category: Czapinska, H.]]
+[[Category: Bochtler M]]
-[[Category: Siksnys, V.]]
+[[Category: Carpenter M]]
-[[Category: Szczepanowski, R H.]]
+[[Category: Czapinska H]]
-[[Category: Tamulaitis, G.]]
+[[Category: Siksnys V]]
-[[Category: Base flipping]]
+[[Category: Szczepanowski RH]]
-[[Category: Endonuclease-dna complex]]
+[[Category: Tamulaitis G]]
-[[Category: Hydrolase-dna complex]]
-[[Category: Pspgi]]
-[[Category: Restriction enzyme]]