3bm3: Difference between revisions
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==Restriction endonuclease PspGI-substrate DNA complex== | ==Restriction endonuclease PspGI-substrate DNA complex== | ||
<StructureSection load='3bm3' size='340' side='right' caption='[[3bm3]], [[Resolution|resolution]] 1.70Å' scene=''> | <StructureSection load='3bm3' size='340' side='right'caption='[[3bm3]], [[Resolution|resolution]] 1.70Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3bm3]] is a 4 chain structure with sequence from [ | <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> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7Å</td></tr> | ||
<tr id=' | <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> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <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> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/O93646_9EURY O93646_9EURY] | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bm/3bm3_consurf.spt"</scriptWhenChecked> | <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/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </jmolCheckbox> | ||
| Line 20: | Line 22: | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == 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. | |||
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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 3bm3" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 3bm3" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Endonuclease 3D structures|Endonuclease 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Pyrococcus sp. | [[Category: Large Structures]] | ||
[[Category: Bhagwat | [[Category: Pyrococcus sp. GI-H]] | ||
[[Category: Bochtler | [[Category: Bhagwat A]] | ||
[[Category: Carpenter | [[Category: Bochtler M]] | ||
[[Category: Czapinska | [[Category: Carpenter M]] | ||
[[Category: Siksnys | [[Category: Czapinska H]] | ||
[[Category: Szczepanowski | [[Category: Siksnys V]] | ||
[[Category: Tamulaitis | [[Category: Szczepanowski RH]] | ||
[[Category: Tamulaitis G]] | |||
Latest revision as of 04:38, 21 November 2024
Restriction endonuclease PspGI-substrate DNA complexRestriction endonuclease PspGI-substrate DNA complex
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedAn 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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