1dc1: Difference between revisions

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[[Image:1dc1.gif|left|200px]]<br /><applet load="1dc1" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:1dc1.gif|left|200px]]<br /><applet load="1dc1" size="350" color="white" frame="true" align="right" spinBox="true"

caption="1dc1, resolution 1.70Å" />

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

==Overview==

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.

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 Structure==

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].

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 <scene name='pdbligand=DIO:'>DIO</scene> 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA].

==Reference==

Line 14:

[[Category: Single protein]]

[[Category: Type II site-specific deoxyribonuclease]]

[[Category: Friedman, A.M.]]

[[Category: Friedman, A M.]]

[[Category: Pelletier, J.J.]]

[[Category: Pelletier, J J.]]

[[Category: Woerd, M.J.van.der.]]

[[Category: Woerd, M J.van der.]]

[[Category: Xu, S.Y.]]

[[Category: Xu, S Y.]]

[[Category: DIO]]

[[Category: degenerate dna recognition]]

Line 24:

[[Category: thermophilic enzyme]]

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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:15:04 2008''

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@@ Line 1: / Line 1: @@
-[[Image:1dc1.gif|left|200px]]<br /><applet load="1dc1" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1dc1.gif|left|200px]]<br /><applet load="1dc1" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1dc1, resolution 1.70&Aring;" />
 '''RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD'''<br />
 ==Overview==
-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.
+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 Structure==
-DC1 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].
+DC1 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 <scene name='pdbligand=DIO:'>DIO</scene> 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC1 OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Single protein]]
 [[Category: Type II site-specific deoxyribonuclease]]
-[[Category: Friedman, A.M.]]
+[[Category: Friedman, A M.]]
-[[Category: Pelletier, J.J.]]
+[[Category: Pelletier, J J.]]
-[[Category: Woerd, M.J.van.der.]]
+[[Category: Woerd, M J.van der.]]
-[[Category: Xu, S.Y.]]
+[[Category: Xu, S Y.]]
 [[Category: DIO]]
 [[Category: degenerate dna recognition]]
@@ Line 24: / Line 24: @@
 [[Category: thermophilic enzyme]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:09:19 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:15:04 2008''