1dc1

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(New page: 200px<br /><applet load="1dc1" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dc1, resolution 1.70&Aring;" /> '''RESTRICTION ENZYME B...)
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[[Image:1dc1.gif|left|200px]]<br /><applet load="1dc1" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1dc1, resolution 1.70&Aring;" />
 
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'''RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD'''<br />
 
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==Overview==
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==RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD==
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BACKGROUND: Restriction endonucleases form a diverse family of proteins, with substantial variation in sequence, structure, and interaction with, recognition site DNA. BsoBI is a thermophilic restriction endonuclease, that exhibits both base-specific and degenerate recognition within the, sequence CPyCGPuG. RESULTS: The structure of BsoBI complexed to cognate, DNA has been determined to 1.7 A resolution, revealing several, unprecedented features. Each BsoBI monomer is formed by inserting a, helical domain into an expanded EcoRI-type catalytic domain. DNA is, completely encircled by a BsoBI dimer. Recognition sequence DNA lies, within a 20 A long tunnel of protein that excludes bulk solvent., Interactions with the specific bases are made in both grooves through, direct and water-mediated hydrogen bonding. Interaction with the, degenerate position is mediated by a purine-specific hydrogen bond to N7, ensuring specificity, and water-mediated H bonding to the purine N6/O6 and, pyrimidine N4/O4, allowing degeneracy. In addition to the conserved active, site residues of the DX(n)(E/D)ZK restriction enzyme motif, His253 is, positioned to act as a general base. CONCLUSIONS: A catalytic mechanism, employing His253 and two metal ions is proposed. If confirmed, this would, be the first example of histidine-mediated catalysis in a restriction, endonuclease. The structure also provides two novel examples of the role, of water in protein-DNA interaction. Degenerate recognition may be, mediated by employing water as a hydrogen bond donor or acceptor. The, structure of DNA in the tunnel may also be influenced by the absence of, bulk solvent.
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<StructureSection load='1dc1' size='340' side='right'caption='[[1dc1]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1dc1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DC1 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc1 OCA], [https://pdbe.org/1dc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dc1 RCSB], [https://www.ebi.ac.uk/pdbsum/1dc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dc1 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/T2B1_GEOSE T2B1_GEOSE] Recognizes the double-stranded sequence CYCGRG and cleaves after C-1.
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==About this Structure==
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==See Also==
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1DC1 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] with DIO as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA].
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis., van der Woerd MJ, Pelletier JJ, Xu S, Friedman AM, Structure. 2001 Feb 7;9(2):133-44. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11250198 11250198]
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[[Category: Geobacillus stearothermophilus]]
[[Category: Geobacillus stearothermophilus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Type II site-specific deoxyribonuclease]]
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[[Category: Friedman AM]]
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[[Category: Friedman, A.M.]]
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[[Category: Pelletier JJ]]
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[[Category: Pelletier, J.J.]]
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[[Category: Xu S-Y]]
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[[Category: Woerd, M.J.van.der.]]
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[[Category: Van der Woerd MJ]]
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[[Category: Xu, S.Y.]]
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[[Category: DIO]]
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[[Category: degenerate dna recognition]]
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[[Category: protein-dna complex]]
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[[Category: restriction endonuclease]]
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[[Category: thermophilic enzyme]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:09:19 2007''
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Current revision

RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD

PDB ID 1dc1

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