3gox

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[[Image:3gox.png|left|200px]]
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==Crystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99I in the absence of EDTA==
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<StructureSection load='3gox' size='340' side='right' caption='[[3gox]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3gox]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GOX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GOX FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3fc3|3fc3]], [[2qnf|2qnf]], [[2qnc|2qnc]], [[1a73|1a73]]</td></tr>
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<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">jhp_0755, synthetic gene codon optimized for Escherichia coli ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 Helicobacter pylori])</td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3gox FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gox OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gox RCSB], [http://www.ebi.ac.uk/pdbsum/3gox PDBsum]</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/go/3gox_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/chain_selection.php?pdb_ID=2ata 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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The 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).
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<!--
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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<ref>PMID:19380375</ref>
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The line below this paragraph, containing "STRUCTURE_3gox", creates the "Structure Box" on the page.
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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or leave the SCENE parameter empty for the default display.
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-->
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{{STRUCTURE_3gox| PDB=3gox | SCENE= }}
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===Crystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99I in the absence of EDTA===
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<!--
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<references/>
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The line below this paragraph, {{ABSTRACT_PUBMED_19380375}}, adds the Publication Abstract to the page
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__TOC__
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(as it appears on PubMed at http://www.pubmed.gov), where 19380375 is the PubMed ID number.
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</StructureSection>
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-->
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{{ABSTRACT_PUBMED_19380375}}
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==About this Structure==
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[[3gox]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GOX OCA].
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==Reference==
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<ref group="xtra">PMID:019380375</ref><ref group="xtra">PMID:017873859</ref><ref group="xtra">PMID:009665136</ref><ref group="xtra">PMID:019351152</ref><references group="xtra"/>
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[[Category: Helicobacter pylori]]
[[Category: Helicobacter pylori]]
[[Category: Bochtler, M.]]
[[Category: Bochtler, M.]]

Revision as of 09:52, 21 May 2014

Crystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99I in the absence of EDTA

3gox, resolution 1.50Å

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