1dc1: Difference between revisions
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[[Image:1dc1.gif|left|200px]] | [[Image:1dc1.gif|left|200px]] | ||
'''RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD''' | {{Structure | ||
|PDB= 1dc1 |SIZE=350|CAPTION= <scene name='initialview01'>1dc1</scene>, resolution 1.70Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=DIO:1,4-DIETHYLENE DIOXIDE'>DIO</scene> | |||
|ACTIVITY= [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] | |||
|GENE= | |||
}} | |||
'''RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1DC1 is a [ | 1DC1 is a [[Single protein]] structure of sequence from [http://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]. | ||
==Reference== | ==Reference== | ||
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:// | 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://www.ncbi.nlm.nih.gov/pubmed/11250198 11250198] | ||
[[Category: Geobacillus stearothermophilus]] | [[Category: Geobacillus stearothermophilus]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: thermophilic enzyme]] | [[Category: thermophilic enzyme]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:36:02 2008'' | ||
Revision as of 11:36, 20 March 2008
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| , resolution 1.70Å | |||||||
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| Ligands: | |||||||
| Activity: | Type II site-specific deoxyribonuclease, with EC number 3.1.21.4 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD
OverviewOverview
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.
About this StructureAbout this Structure
1DC1 is a Single protein structure of sequence from Geobacillus stearothermophilus. Full crystallographic information is available from OCA.
ReferenceReference
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:11250198
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