1dfm
From Proteopedia
(New page: 200px<br /><applet load="1dfm" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dfm, resolution 1.5Å" /> '''CRYSTAL STRUCTURE OF ...) |
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| - | [[Image:1dfm.gif|left|200px]]<br /><applet load="1dfm" size=" | + | [[Image:1dfm.gif|left|200px]]<br /><applet load="1dfm" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1dfm, resolution 1.5Å" /> | caption="1dfm, resolution 1.5Å" /> | ||
'''CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE BGLII COMPLEXED WITH DNA 16-MER'''<br /> | '''CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE BGLII COMPLEXED WITH DNA 16-MER'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Restriction endonucleases are remarkably resilient to alterations in their | + | Restriction endonucleases are remarkably resilient to alterations in their DNA binding specificity. To understand the basis of this immutability, we have determined the crystal structure of endonuclease BglII bound to its recognition sequence (AGATCT), at 1. 5 A resolution. We compare the structure of BglII to endonuclease BamHI, which recognizes a closely related DNA site (GGATCC). We show that both enzymes share a similar alpha/beta core, but in BglII, the core is augmented by a beta-sandwich domain that encircles the DNA to provide extra specificity. Remarkably, the DNA is contorted differently in the two structures, leading to different protein-DNA contacts for even the common base pairs. Furthermore, the BglII active site contains a glutamine in place of the glutamate at the general base position in BamHI, and only a single metal is found coordinated to the putative nucleophilic water and the phosphate oxygens. This surprising diversity in structures shows that different strategies can be successful in achieving site-specific recognition and catalysis in restriction endonucleases. |
==About this Structure== | ==About this Structure== | ||
| - | 1DFM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1DFM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DFM OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Bacillus subtilis]] | [[Category: Bacillus subtilis]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Aggarwal, A | + | [[Category: Aggarwal, A K.]] |
[[Category: Kucera, R.]] | [[Category: Kucera, R.]] | ||
| - | [[Category: Lukacs, C | + | [[Category: Lukacs, C M.]] |
[[Category: Schildkraut, I.]] | [[Category: Schildkraut, I.]] | ||
[[Category: CA]] | [[Category: CA]] | ||
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[[Category: restriction enzyme]] | [[Category: restriction enzyme]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:16:13 2008'' |
Revision as of 10:16, 21 February 2008
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CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE BGLII COMPLEXED WITH DNA 16-MER
Overview
Restriction endonucleases are remarkably resilient to alterations in their DNA binding specificity. To understand the basis of this immutability, we have determined the crystal structure of endonuclease BglII bound to its recognition sequence (AGATCT), at 1. 5 A resolution. We compare the structure of BglII to endonuclease BamHI, which recognizes a closely related DNA site (GGATCC). We show that both enzymes share a similar alpha/beta core, but in BglII, the core is augmented by a beta-sandwich domain that encircles the DNA to provide extra specificity. Remarkably, the DNA is contorted differently in the two structures, leading to different protein-DNA contacts for even the common base pairs. Furthermore, the BglII active site contains a glutamine in place of the glutamate at the general base position in BamHI, and only a single metal is found coordinated to the putative nucleophilic water and the phosphate oxygens. This surprising diversity in structures shows that different strategies can be successful in achieving site-specific recognition and catalysis in restriction endonucleases.
About this Structure
1DFM is a Single protein structure of sequence from Bacillus subtilis with as ligand. Full crystallographic information is available from OCA.
Reference
Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution., Lukacs CM, Kucera R, Schildkraut I, Aggarwal AK, Nat Struct Biol. 2000 Feb;7(2):134-40. PMID:10655616
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