3fc3: Difference between revisions

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-[[Image:3fc3.png|left|200px]]
-<!--
+==Crystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99I==
-The line below this paragraph, containing "STRUCTURE_3fc3", creates the "Structure Box" on the page.
+<StructureSection load='3fc3' size='340' side='right'caption='[[3fc3]], [[Resolution|resolution]] 1.75&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'>[[3fc3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_J99 Helicobacter 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>
-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]] 1.75&#8491;</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>
-{{STRUCTURE_3fc3|  PDB=3fc3  |  SCENE=  }}
+<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>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9ZL26_HELPJ Q9ZL26_HELPJ]
+== 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/fc/3fc3_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=3fc3 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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).
-===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 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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3fc3" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19380375}}, adds the Publication Abstract to the page
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19380375 is the PubMed ID number.
+*[[Integrin 3D structures|Integrin 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_19380375}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-[[3fc3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori_j99 Helicobacter pylori j99]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FC3 OCA].
+[[Category: Helicobacter pylori J99]]
+[[Category: Large Structures]]
-==Reference==
+[[Category: Bochtler M]]
-<ref group="xtra">PMID:19380375</ref><ref group="xtra">PMID:17873859</ref><ref group="xtra">PMID:9665136</ref><references group="xtra"/>
+[[Category: Czapinska H]]
-[[Category: Helicobacter pylori j99]]
+[[Category: Sokolowska M]]
-[[Category: Bochtler, M.]]
-[[Category: Czapinska, H.]]
-[[Category: Sokolowska, M.]]
-[[Category: Endonuclease-dna complex]]
-[[Category: Hpy99i]]
-[[Category: Hydrolase/dna complex]]
-[[Category: Pseudopalindrome]]
-[[Category: Restriction enzyme]]