2fkh: Difference between revisions
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==Crystal Form II of Pre-Reactive Complex of Restriction Endonuclease HinP1I with Cognate DNA and Calcium Ions== | ==Crystal Form II of Pre-Reactive Complex of Restriction Endonuclease HinP1I with Cognate DNA and Calcium Ions== | ||
<StructureSection load='2fkh' size='340' side='right' caption='[[2fkh]], [[Resolution|resolution]] 3.09Å' scene=''> | <StructureSection load='2fkh' size='340' side='right'caption='[[2fkh]], [[Resolution|resolution]] 3.09Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2fkh]] is a 3 chain structure with sequence from [ | <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> | ||
</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]] 3.09Å</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> | |||
<tr id=' | <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> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q5I6E6_HAEIF Q5I6E6_HAEIF] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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==See Also== | ==See Also== | ||
*[[Endonuclease|Endonuclease]] | *[[Endonuclease 3D structures|Endonuclease 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Haemophilus influenzae]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Horton | [[Category: Horton JR]] | ||
Latest revision as of 12:28, 30 August 2023
Crystal Form II of Pre-Reactive Complex of Restriction Endonuclease HinP1I with Cognate DNA and Calcium IonsCrystal Form II of Pre-Reactive Complex of Restriction Endonuclease HinP1I with Cognate DNA and Calcium Ions
Structural highlights
FunctionPublication Abstract from PubMedHinP1I 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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