1dc1: Difference between revisions

Revision as of 13:40, 2 May 2008

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 Page seeded by OCA on Fri May 2 13:40:35 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 [[Image:1dc1.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 1dc1 |SIZE=350|CAPTION= <scene name='initialview01'>1dc1</scene>, resolution 1.70&Aring;
+The line below this paragraph, containing "STRUCTURE_1dc1", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <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>
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_1dc1|  PDB=1dc1  |  SCENE=  }}
-|RELATEDENTRY=
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc1 OCA], [http://www.ebi.ac.uk/pdbsum/1dc1 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1dc1 RCSB]</span>
-}}
 '''RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD'''
@@ Line 30: / Line 27: @@
 [[Category: Woerd, M J.van der.]]
 [[Category: Xu, S Y.]]
-[[Category: degenerate dna recognition]]
+[[Category: Degenerate dna recognition]]
-[[Category: protein-dna complex]]
+[[Category: Protein-dna complex]]
-[[Category: restriction endonuclease]]
+[[Category: Restriction endonuclease]]
-[[Category: thermophilic enzyme]]
+[[Category: Thermophilic enzyme]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 13:40:35 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:38:37 2008''