1bsu
From Proteopedia
(New page: 200px<br /><applet load="1bsu" size="450" color="white" frame="true" align="right" spinBox="true" caption="1bsu, resolution 2.0Å" /> '''STRUCTURAL AND ENERGE...) |
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| - | [[Image:1bsu.gif|left|200px]]<br /><applet load="1bsu" size=" | + | [[Image:1bsu.gif|left|200px]]<br /><applet load="1bsu" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1bsu, resolution 2.0Å" /> | caption="1bsu, resolution 2.0Å" /> | ||
'''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== | ||
| - | 1BSU is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with CA 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:// | + | 1BSU is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=CA:'>CA</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=1BSU 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: CA]] | [[Category: CA]] | ||
| - | [[Category: complex endonuclease ecorv (3 | + | [[Category: complex endonuclease ecorv (3 1.21 4)/dna]] |
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:58:42 2008'' |
Revision as of 09:58, 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
1BSU is a Single protein structure of sequence from Escherichia coli with as ligand. 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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