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3nic
From Proteopedia
(Difference between revisions)
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==DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29kI inactive variant Y49F== | ==DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29kI inactive variant Y49F== | ||
| - | <StructureSection load='3nic' size='340' side='right' caption='[[3nic]], [[Resolution|resolution]] 2.80Å' scene=''> | + | <StructureSection load='3nic' size='340' side='right'caption='[[3nic]], [[Resolution|resolution]] 2.80Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[3nic]] is a 16 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[3nic]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NIC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NIC 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]] 2.8Å</td></tr> |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=3nic FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nic OCA], [https://pdbe.org/3nic PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nic RCSB], [https://www.ebi.ac.uk/pdbsum/3nic PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nic ProSAT]</span></td></tr> |
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| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | |
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/Q46944_ECOLX Q46944_ECOLX] | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3nic ConSurf]. | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3nic ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | The GIY-YIG endonuclease family comprises hundreds of diverse proteins and a multitude of functions; none have been visualized bound to DNA. The structure of the GIY-YIG restriction endonuclease R.Eco29kI has been solved both alone and bound to its target site. The protein displays a domain-swapped homodimeric structure with several extended surface loops encircling the DNA. Only three side chains from each protein subunit contact DNA bases, two directly and one via a bridging solvent molecule. Both tyrosine residues within the GIY-YIG motif are positioned in the catalytic center near a putative nucleophilic water; the remainder of the active site resembles the HNH endonuclease family. The structure illustrates how the GIY-YIG scaffold has been adapted for the highly specific recognition of a DNA restriction site, in contrast to nonspecific DNA cleavage by GIY-YIG domains in homing endonucleases or structure-specific cleavage by DNA repair enzymes such as UvrC. | ||
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| - | Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI.,Mak AN, Lambert AR, Stoddard BL Structure. 2010 Aug 25. PMID:20800503<ref>PMID:20800503</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 3nic" style="background-color:#fffaf0;"></div> | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Escherichia coli]] |
| - | [[Category: | + | [[Category: Large Structures]] |
| - | [[Category: Lambert | + | [[Category: Lambert AR]] |
| - | [[Category: Mak | + | [[Category: Mak ANS]] |
| - | [[Category: Stoddard | + | [[Category: Stoddard BL]] |
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Current revision
DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29kI inactive variant Y49F
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