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==Post-Reactive Complex of Restriction Endonuclease HinP1I with Nicked Cognate DNA and Magnesium Ions== | ==Post-Reactive Complex of Restriction Endonuclease HinP1I with Nicked Cognate DNA and Magnesium Ions== | ||
<StructureSection load='2flc' size='340' side='right' caption='[[2flc]], [[Resolution|resolution]] 2.59Å' scene=''> | <StructureSection load='2flc' size='340' side='right'caption='[[2flc]], [[Resolution|resolution]] 2.59Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2flc]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2flc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacterium_influenzae"_lehmann_and_neumann_1896 "bacterium influenzae" lehmann and neumann 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FLC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FLC FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ynm|1ynm]], [[2fkc|2fkc]], [[2fkh|2fkh]], [[2fl3|2fl3]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ynm|1ynm]], [[2fkc|2fkc]], [[2fkh|2fkh]], [[2fl3|2fl3]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hinP1IR ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hinP1IR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 "Bacterium influenzae" Lehmann and Neumann 1896])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4] </span></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=2flc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2flc OCA], [https://pdbe.org/2flc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2flc RCSB], [https://www.ebi.ac.uk/pdbsum/2flc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2flc ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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</div> | </div> | ||
<div class="pdbe-citations 2flc" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 2flc" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Endonuclease 3D structures|Endonuclease 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Bacterium influenzae lehmann and neumann 1896]] | [[Category: Bacterium influenzae lehmann and neumann 1896]] | ||
[[Category: Large Structures]] | |||
[[Category: Type II site-specific deoxyribonuclease]] | [[Category: Type II site-specific deoxyribonuclease]] | ||
[[Category: Horton, J R]] | [[Category: Horton, J R]] | ||
Revision as of 18:28, 3 March 2021
Post-Reactive Complex of Restriction Endonuclease HinP1I with Nicked Cognate DNA and Magnesium IonsPost-Reactive Complex of Restriction Endonuclease HinP1I with Nicked Cognate DNA and Magnesium Ions
Structural highlights
Publication 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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