2fkh: Difference between revisions

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-{{Seed}}
-[[Image:2fkh.png|left|200px]]
-<!--
+==Crystal Form II of Pre-Reactive Complex of Restriction Endonuclease HinP1I with Cognate DNA and Calcium Ions==
-The line below this paragraph, containing "STRUCTURE_2fkh", creates the "Structure Box" on the page.
+<StructureSection load='2fkh' size='340' side='right'caption='[[2fkh]], [[Resolution|resolution]] 3.09&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'>[[2fkh]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FKH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FKH 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]] 3.09&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-{{STRUCTURE_2fkh|  PDB=2fkh  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2fkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fkh OCA], [https://pdbe.org/2fkh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fkh RCSB], [https://www.ebi.ac.uk/pdbsum/2fkh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fkh ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q5I6E6_HAEIF Q5I6E6_HAEIF]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+HinP1I recognizes and cleaves the palindromic tetranucleotide sequence G downward arrowCGC in DNA. We report three structures of HinP1I-DNA complexes: in the presence of Ca(2+) (pre-reactive complex), in the absence of metal ion (binary complex) and in the presence of Mg(2+) (post-reactive complex). HinP1I forms a back-to-back dimer with two active sites and two DNA duplexes bound on the outer surfaces of the dimer facing away from each other. The 10 bp DNA duplexes undergo protein-induced distortions exhibiting features of A-, B- and Z-conformations: bending on one side (by intercalation of a phenylalanine side chain into the major groove), base flipping on the other side of the recognition site (by expanding the step rise distance of the local base pair to Z-form) and a local A-form conformation between the two central C:G base pairs of the recognition site (by binding of the N-terminal helix in the minor groove). In the pre- and post-reactive complexes, two metals (Ca(2+) or Mg(2+)) are found in the active site. The enzyme appears to cleave DNA sequentially, hydrolyzing first one DNA strand, as seen in the post-reactive complex in the crystalline state, and then the other, as supported by the observation that, in solution, a nicked DNA intermediate accumulates before linearization.
-===Crystal Form II of Pre-Reactive Complex of Restriction Endonuclease HinP1I with Cognate DNA and Calcium Ions===
+DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion.,Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG, Roberts RJ, Cheng X Nucleic Acids Res. 2006 Feb 9;34(3):939-48. Print 2006. PMID:16473850<ref>PMID:16473850</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2fkh" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16473850}}, adds the Publication Abstract to the page
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16473850 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16473850}}
+__TOC__
+</StructureSection>
-==About this Structure==
-FKH is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FKH OCA].
-==Reference==
-DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion., Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG, Roberts RJ, Cheng X, Nucleic Acids Res. 2006 Feb 9;34(3):939-48. Print 2006. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16473850 16473850]
 [[Category: Haemophilus influenzae]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Type II site-specific deoxyribonuclease]]
+[[Category: Horton JR]]
-[[Category: Horton, J R.]]
-[[Category: Dna superhelix]]
-[[Category: Protein dimerizaton]]
-[[Category: Protein-dna-metal ion complex]]
-[[Category: Restriction endonuclease]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 21:21:48 2008''