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| | ==HincII bound to cleaved cognate DNA GTCGAC and Mn2+== | | ==HincII bound to cleaved cognate DNA GTCGAC and Mn2+== |
| - | <StructureSection load='1xhv' size='340' side='right' caption='[[1xhv]], [[Resolution|resolution]] 2.50Å' scene=''> | + | <StructureSection load='1xhv' size='340' side='right'caption='[[1xhv]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1xhv]] is a 12 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=1XHV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XHV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1xhv]] is a 12 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=1XHV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XHV FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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]] 2.5Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kc6|1kc6]], [[1tw8|1tw8]], [[1xhu|1xhu]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=1xhv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xhv OCA], [https://pdbe.org/1xhv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xhv RCSB], [https://www.ebi.ac.uk/pdbsum/1xhv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xhv 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=1xhv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xhv OCA], [http://pdbe.org/1xhv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xhv RCSB], [http://www.ebi.ac.uk/pdbsum/1xhv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xhv ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/T2C2_HAEIF T2C2_HAEIF]] 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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 1xhv" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 1xhv" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Endonuclease 3D structures|Endonuclease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacterium influenzae lehmann and neumann 1896]] | + | [[Category: Haemophilus influenzae]] |
| - | [[Category: Type II site-specific deoxyribonuclease]] | + | [[Category: Large Structures]] |
| - | [[Category: Etzkorn, C]] | + | [[Category: Etzkorn C]] |
| - | [[Category: Horton, N C]] | + | [[Category: Horton NC]] |
| - | [[Category: Hydrolase-dna complex]]
| + | |
| - | [[Category: Phosphoryl transfer]]
| + | |
| - | [[Category: Restriction endonuclease]]
| + | |
| Structural highlights
Function
T2C2_HAEIF Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3.
Publication Abstract from PubMed
The three-dimensional X-ray crystal structures of HincII bound to cognate DNA containing GTCGAC and Mn(2+) or Mg(2+), at 2.50A and 2.95A resolution, respectively, are presented. In both structures, the DNA is found cleaved, and the positions of the active-site groups, cleaved phosphate group, and 3' oxygen atom of the leaving group are in very similar positions. Two highly occupied Mn(2+) positions are found in each active site of the four crystallographically independent subunit copies in the HincII/DNA/Mn(2+) structure. The manganese ion closest to the previously identified single Ca(2+) position of HincII is shifted 1.7A and has lost direct ligation to the active-site aspartate residue, Asp127. A Mn(2+)-ligated water molecule in a position analogous to that seen in the HincII/DNA/Ca(2+) structure, and proposed to be the attacking nucleophile, is beyond hydrogen bonding distance from the active-site lysine residue, Lys129, but remains within hydrogen bonding distance from the proRp oxygen atom of the phosphate group 3' to the scissile phosphate group. In addition, the position of the cleaved phosphate group is on the opposite side of the axis connecting the two metal ions relative to that found in the BamHI/product DNA/Mn(2+) structure. Mechanistic implications are discussed, and a model for the two-metal-ion mechanism of DNA cleavage by HincII is proposed.
Mechanistic insights from the structures of HincII bound to cognate DNA cleaved from addition of Mg2+ and Mn2+.,Etzkorn C, Horton NC J Mol Biol. 2004 Oct 29;343(4):833-49. PMID:15476804[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Etzkorn C, Horton NC. Mechanistic insights from the structures of HincII bound to cognate DNA cleaved from addition of Mg2+ and Mn2+. J Mol Biol. 2004 Oct 29;343(4):833-49. PMID:15476804 doi:S0022-2836(04)01082-4
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