3fc3: Difference between revisions
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==Crystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99I== | ==Crystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99I== | ||
<StructureSection load='3fc3' size='340' side='right' caption='[[3fc3]], [[Resolution|resolution]] 1.75Å' scene=''> | <StructureSection load='3fc3' size='340' side='right'caption='[[3fc3]], [[Resolution|resolution]] 1.75Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3fc3]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3fc3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Campylobacter_pylori_j99 Campylobacter pylori j99]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FC3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FC3 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2qnf|2qnf]], [[2qnc|2qnc]], [[1a73|1a73]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2qnf|2qnf]], [[2qnc|2qnc]], [[1a73|1a73]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">jhp_0755, synthetic gene codon optimized for Escherichia coli ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">jhp_0755, synthetic gene codon optimized for Escherichia coli ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85963 Campylobacter pylori J99])</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=3fc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fc3 OCA], [https://pdbe.org/3fc3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fc3 RCSB], [https://www.ebi.ac.uk/pdbsum/3fc3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fc3 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fc/3fc3_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fc/3fc3_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
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</div> | </div> | ||
<div class="pdbe-citations 3fc3" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 3fc3" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Endonuclease 3D structures|Endonuclease 3D structures]] | |||
*[[Integrin 3D structures|Integrin 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Campylobacter pylori j99]] | [[Category: Campylobacter pylori j99]] | ||
[[Category: Large Structures]] | |||
[[Category: Bochtler, M]] | [[Category: Bochtler, M]] | ||
[[Category: Czapinska, H]] | [[Category: Czapinska, H]] | ||
Revision as of 10:57, 2 March 2022
Crystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99ICrystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99I
Structural highlights
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 beta beta alpha-Me restriction endonuclease (REase) Hpy99I recognizes the CGWCG target sequence and cleaves it with unusual stagger (five nucleotide 5'-recessed ends). Here we present the crystal structure of the specific complex of the dimeric enzyme with DNA. The Hpy99I protomer consists of an antiparallel beta-barrel and two beta 4 alpha 2 repeats. Each repeat coordinates a structural zinc ion with four cysteine thiolates in two CXXC motifs. The beta beta alpha-Me region of the second beta 4 alpha 2 repeat holds the catalytic metal ion (or its sodium surrogate) via Asp148 and Asn165 and activates a water molecule with the general base His149. In the specific complex, Hpy99I forms a ring-like structure around the DNA that contacts DNA bases on the major and minor groove sides via the first and second beta 4 alpha 2 repeats, respectively. Hpy99I interacts with the central base pair of the recognition sequence only on the minor groove side, where A:T resembles T:A and G:C is similar to C:G. The Hpy99I-DNA co-crystal structure provides the first detailed illustration of the beta beta alpha-Me site in REases and complements structural information on the use of this active site motif in other groups of endonucleases such as homing endonucleases (e.g. I-PpoI) and Holliday junction resolvases (e.g. T4 endonuclease VII). Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA.,Sokolowska M, Czapinska H, Bochtler M Nucleic Acids Res. 2009 Jun;37(11):3799-810. Epub 2009 Apr 20. PMID:19380375[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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