6ukf: Difference between revisions
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<StructureSection load='6ukf' size='340' side='right'caption='[[6ukf]], [[Resolution|resolution]] 1.00Å' scene=''> | <StructureSection load='6ukf' size='340' side='right'caption='[[6ukf]], [[Resolution|resolution]] 1.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6ukf]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UKF OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6ukf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_parahaemolyticus Haemophilus parahaemolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UKF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UKF FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4 | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=6ukf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ukf OCA], [https://pdbe.org/6ukf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ukf RCSB], [https://www.ebi.ac.uk/pdbsum/6ukf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ukf ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/I3DBY6_HAEPH I3DBY6_HAEPH] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
HhaI, a Type II restriction endonuclease, recognizes the symmetric sequence 5'-GCG downward arrowC-3' in duplex DNA and cleaves (' downward arrow') to produce fragments with 2-base, 3'-overhangs. We determined the structure of HhaI in complex with cognate DNA at an ultra-high atomic resolution of 1.0 A. Most restriction enzymes act as dimers with two catalytic sites, and cleave the two strands of duplex DNA simultaneously, in a single binding event. HhaI, in contrast, acts as a monomer with only one catalytic site, and cleaves the DNA strands sequentially, one after the other. HhaI comprises three domains, each consisting of a mixed five-stranded beta sheet with a defined function. The first domain contains the catalytic-site; the second contains residues for sequence recognition; and the third contributes to non-specific DNA binding. The active-site belongs to the 'PD-D/EXK' superfamily of nucleases and contains the motif SD-X11-EAK. The first two domains are similar in structure to two other monomeric restriction enzymes, HinP1I (G downward arrowCGC) and MspI (C downward arrowCGG), which produce fragments with 5'-overhangs. The third domain, present only in HhaI, shifts the positions of the recognition residues relative to the catalytic site enabling this enzyme to cleave the recognition sequence at a different position. The structure of M.HhaI, the biological methyltransferase partner of HhaI, was determined earlier. Together, these two structures represent the first natural pair of restriction-modification enzymes to be characterized in atomic detail. | |||
Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 A.,Horton JR, Yang J, Zhang X, Petronzio T, Fomenkov A, Wilson GG, Roberts RJ, Cheng X Nucleic Acids Res. 2019 Dec 27. pii: 5687824. doi: 10.1093/nar/gkz1195. PMID:31879785<ref>PMID:31879785</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6ukf" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Endonuclease 3D structures|Endonuclease 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Haemophilus parahaemolyticus]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Cheng | [[Category: Cheng X]] | ||
[[Category: Horton | [[Category: Horton JR]] | ||
Latest revision as of 10:53, 11 October 2023
HhaI endonuclease in Complex with DNA at 1 Angstrom ResolutionHhaI endonuclease in Complex with DNA at 1 Angstrom Resolution
Structural highlights
FunctionPublication Abstract from PubMedHhaI, a Type II restriction endonuclease, recognizes the symmetric sequence 5'-GCG downward arrowC-3' in duplex DNA and cleaves (' downward arrow') to produce fragments with 2-base, 3'-overhangs. We determined the structure of HhaI in complex with cognate DNA at an ultra-high atomic resolution of 1.0 A. Most restriction enzymes act as dimers with two catalytic sites, and cleave the two strands of duplex DNA simultaneously, in a single binding event. HhaI, in contrast, acts as a monomer with only one catalytic site, and cleaves the DNA strands sequentially, one after the other. HhaI comprises three domains, each consisting of a mixed five-stranded beta sheet with a defined function. The first domain contains the catalytic-site; the second contains residues for sequence recognition; and the third contributes to non-specific DNA binding. The active-site belongs to the 'PD-D/EXK' superfamily of nucleases and contains the motif SD-X11-EAK. The first two domains are similar in structure to two other monomeric restriction enzymes, HinP1I (G downward arrowCGC) and MspI (C downward arrowCGG), which produce fragments with 5'-overhangs. The third domain, present only in HhaI, shifts the positions of the recognition residues relative to the catalytic site enabling this enzyme to cleave the recognition sequence at a different position. The structure of M.HhaI, the biological methyltransferase partner of HhaI, was determined earlier. Together, these two structures represent the first natural pair of restriction-modification enzymes to be characterized in atomic detail. Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 A.,Horton JR, Yang J, Zhang X, Petronzio T, Fomenkov A, Wilson GG, Roberts RJ, Cheng X Nucleic Acids Res. 2019 Dec 27. pii: 5687824. doi: 10.1093/nar/gkz1195. PMID:31879785[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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