1bsu

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[[Image:1bsu.gif|left|200px]]
[[Image:1bsu.gif|left|200px]]
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{{Structure
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<!--
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|PDB= 1bsu |SIZE=350|CAPTION= <scene name='initialview01'>1bsu</scene>, resolution 2.0&Aring;
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The line below this paragraph, containing "STRUCTURE_1bsu", creates the "Structure Box" on the page.
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|SITE=
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=5CM:5-METHYL-2&#39;-DEOXY-CYTIDINE-5&#39;-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <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=DI:2&#39;-DEOXYINOSINE-5&#39;-MONOPHOSPHATE'>DI</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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|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>
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or leave the SCENE parameter empty for the default display.
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|GENE=
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-->
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|DOMAIN=
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{{STRUCTURE_1bsu| PDB=1bsu | SCENE= }}
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|RELATEDENTRY=
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1bsu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bsu OCA], [http://www.ebi.ac.uk/pdbsum/1bsu PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1bsu RCSB]</span>
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}}
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'''STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASE'''
'''STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASE'''
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[[Category: Martin, A M.]]
[[Category: Martin, A M.]]
[[Category: Perona, J J.]]
[[Category: Perona, J J.]]
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[[Category: complex endonuclease ecorv (3 1.21 4)/dna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 11:54:55 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:07:34 2008''
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Revision as of 08:54, 2 May 2008

Image:1bsu.gif

Template:STRUCTURE 1bsu

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. 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 Page seeded by OCA on Fri May 2 11:54:55 2008

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OCA

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