1bua
From Proteopedia
(New page: 200px<br /><applet load="1bua" size="450" color="white" frame="true" align="right" spinBox="true" caption="1bua, resolution 2.15Å" /> '''STRUCTURAL AND ENERG...) |
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| - | [[Image:1bua.gif|left|200px]]<br /><applet load="1bua" size=" | + | [[Image:1bua.gif|left|200px]]<br /><applet load="1bua" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1bua, resolution 2.15Å" /> | caption="1bua, resolution 2.15Å" /> | ||
'''STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASE'''<br /> | '''STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASE'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Specific recognition by EcoRV endonuclease of its cognate, sharply bent | + | 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== | ==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:// | + | 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== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Type II site-specific deoxyribonuclease]] | [[Category: Type II site-specific deoxyribonuclease]] | ||
| - | [[Category: Martin, A | + | [[Category: Martin, A M.]] |
| - | [[Category: Perona, J | + | [[Category: Perona, J J.]] |
| - | [[Category: endonuclease ecorv (e | + | [[Category: endonuclease ecorv (e c.3 1.21 4)/dna complex]] |
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:59:09 2008'' |
Revision as of 09:59, 21 February 2008
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STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASE
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.
About this Structure
1BUA is a Single protein structure of sequence from Escherichia coli. Active as Type II site-specific deoxyribonuclease, with EC number 3.1.21.4 Full crystallographic information is available from OCA.
Reference
Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease., Martin AM, Sam MD, Reich NO, Perona JJ, Nat Struct Biol. 1999 Mar;6(3):269-77. PMID:10074946
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