1bua: Difference between revisions

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

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

caption="1bua, resolution 2.15Å" />

'''STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASE'''<br />

==Overview==

Specific recognition by EcoRV endonuclease of its cognate, sharply bent, GATATC site at the center TA step occurs solely via hydrophobic, interaction with thymine methyl groups. Mechanistic kinetic analyses of, base analog-substituted DNAs at this position reveal that direct readout, provides 5 kcal mol(-1) toward specificity, with an additional 6-10 kcal, mol(-1) arising from indirect readout. Crystal structures of several base, analog complexes show that the major-groove hydrophobic contacts are, crucial to forming required divalent metal-binding sites, and that, indirect readout operates in part through the sequence-dependent, free-energy cost of unstacking the center base-pair step of the DNA.

Specific recognition by EcoRV endonuclease of its cognate, sharply bent GATATC site at the center TA step occurs solely via hydrophobic interaction with thymine methyl groups. Mechanistic kinetic analyses of base analog-substituted DNAs at this position reveal that direct readout provides 5 kcal mol(-1) toward specificity, with an additional 6-10 kcal mol(-1) arising from indirect readout. Crystal structures of several base analog complexes show that the major-groove hydrophobic contacts are crucial to forming required divalent metal-binding sites, and that indirect readout operates in part through the sequence-dependent free-energy cost of unstacking the center base-pair step of the DNA.

==About this Structure==

1BUA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. 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=1BUA OCA].

1BUA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. 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=1BUA OCA].

==Reference==

Line 14:

[[Category: Single protein]]

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

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

[[Category: Martin, A M.]]

[[Category: Perona, J.J.]]

[[Category: Perona, J J.]]

[[Category: endonuclease ecorv (e.c.3.1.21.4)/dna complex]]

[[Category: endonuclease ecorv (e c.3 1.21 4)/dna complex]]

''Page seeded by [http://~~ispc~~.weizmann.ac.il/oca OCA ] on ~~Tue Nov 20~~ 11:55:~~40 2007~~''

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:59:09 2008''

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@@ Line 1: / Line 1: @@
-[[Image:1bua.gif|left|200px]]<br /><applet load="1bua" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1bua.gif|left|200px]]<br /><applet load="1bua" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1bua, resolution 2.15&Aring;" />
 '''STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASE'''<br />
 ==Overview==
-Specific recognition by EcoRV endonuclease of its cognate, sharply bent, GATATC site at the center TA step occurs solely via hydrophobic, interaction with thymine methyl groups. Mechanistic kinetic analyses of, base analog-substituted DNAs at this position reveal that direct readout, provides 5 kcal mol(-1) toward specificity, with an additional 6-10 kcal, mol(-1) arising from indirect readout. Crystal structures of several base, analog complexes show that the major-groove hydrophobic contacts are, crucial to forming required divalent metal-binding sites, and that, indirect readout operates in part through the sequence-dependent, free-energy cost of unstacking the center base-pair step of the DNA.
+Specific recognition by EcoRV endonuclease of its cognate, sharply bent GATATC site at the center TA step occurs solely via hydrophobic interaction with thymine methyl groups. Mechanistic kinetic analyses of base analog-substituted DNAs at this position reveal that direct readout provides 5 kcal mol(-1) toward specificity, with an additional 6-10 kcal mol(-1) arising from indirect readout. Crystal structures of several base analog complexes show that the major-groove hydrophobic contacts are crucial to forming required divalent metal-binding sites, and that indirect readout operates in part through the sequence-dependent free-energy cost of unstacking the center base-pair step of the DNA.
 ==About this Structure==
-BUA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. 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=1BUA OCA].
+BUA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. 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=1BUA OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Single protein]]
 [[Category: Type II site-specific deoxyribonuclease]]
-[[Category: Martin, A.M.]]
+[[Category: Martin, A M.]]
-[[Category: Perona, J.J.]]
+[[Category: Perona, J J.]]
-[[Category: endonuclease ecorv (e.c.3.1.21.4)/dna complex]]
+[[Category: endonuclease ecorv (e c.3 1.21 4)/dna complex]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 11:55:40 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:59:09 2008''