2gii: Difference between revisions

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 ==Q138F HincII bound to cognate DNA GTTAAC==
-<StructureSection load='2gii' size='340' side='right' caption='[[2gii]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='2gii' size='340' side='right'caption='[[2gii]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2gii]] is a 4 chain structure with sequence from [http://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=2GII OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GII FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2gii]] is a 4 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=2GII OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GII FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2gih|2gih]], [[2gig|2gig]], [[1tw8|1tw8]], [[2gie|2gie]], [[2gij|2gij]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hincIIR ([http://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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gii OCA], [https://pdbe.org/2gii PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gii RCSB], [https://www.ebi.ac.uk/pdbsum/2gii PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gii ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2gii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gii OCA], [http://pdbe.org/2gii PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gii RCSB], [http://www.ebi.ac.uk/pdbsum/2gii PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2gii ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/T2D2_HAEIN T2D2_HAEIN]] Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3.
+[https://www.uniprot.org/uniprot/T2C2_HAEIF T2C2_HAEIF] Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3.
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The functional and structural consequences of a mutation of the DNA intercalating residue of HincII, Q138F, are presented. Modeling has suggested that the DNA intercalation by Gln-138 results in DNA distortions potentially used by HincII in indirect readout of its cognate DNA, GTYRAC (Y = C or T, R = A or G) (Horton, N. C., Dorner, L. F., and Perona, J. J. (2002) Nat. Struct. Biol. 9, 42-47). Kinetic data presented here indicate that the mutation of glutamine 138 to phenylalanine (Q138F) results in a change in sequence specificity at the center two base pairs of the cognate recognition site. We show that the preference of HincII for cutting, but not binding, the three cognate sites differing in the center two base pairs has been altered by the mutation Q138F. Five new crystal structures are presented including Q138F HincII bound to GTTAAC and GTCGAC both with and without Ca2+ as well as the structure of wild type HincII bound to GTTAAC. The Q138F HincII/DNA structures show conformational changes in the protein, bound DNA, and at the protein-DNA interface, consistent with the formation of adaptive complexes. Analysis of these structures and the effect of Ca2+ binding on the protein-DNA interface illuminates the origin of the altered specificity by the mutation Q138F in the HincII enzyme.
-Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism.,Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton NC J Biol Chem. 2006 Aug 18;281(33):23852-69. Epub 2006 May 4. PMID:16675462<ref>PMID:16675462</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2gii" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Endonuclease|Endonuclease]]
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacterium influenzae lehmann and neumann 1896]]
+[[Category: Haemophilus influenzae]]
-[[Category: Type II site-specific deoxyribonuclease]]
+[[Category: Large Structures]]
-[[Category: Horton, N C]]
+[[Category: Horton NC]]
-[[Category: Joshi, H K]]
+[[Category: Joshi HK]]
-[[Category: Dna intercalation]]
-[[Category: Endonuclease]]
-[[Category: Hydrolase-dna complex]]
-[[Category: Indirect readout]]
-[[Category: Protein dna complex]]