1bss
From Proteopedia
(New page: 200px<br /><applet load="1bss" size="450" color="white" frame="true" align="right" spinBox="true" caption="1bss, resolution 2.15Å" /> '''ECORV-T93A/DNA/CA2+'...) |
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| - | [[Image:1bss.gif|left|200px]]<br /><applet load="1bss" size=" | + | [[Image:1bss.gif|left|200px]]<br /><applet load="1bss" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1bss, resolution 2.15Å" /> | caption="1bss, resolution 2.15Å" /> | ||
'''ECORV-T93A/DNA/CA2+'''<br /> | '''ECORV-T93A/DNA/CA2+'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The 2.15-A resolution cocrystal structure of EcoRV endonuclease mutant | + | The 2.15-A resolution cocrystal structure of EcoRV endonuclease mutant T93A complexed with DNA and Ca2+ ions reveals two divalent metals bound in one of the active sites. One of these metals is ligated through an inner-sphere water molecule to the phosphate group located 3' to the scissile phosphate. A second inner-sphere water on this metal is positioned approximately in-line for attack on the scissile phosphate. This structure corroborates the observation that the pro-SP phosphoryl oxygen on the adjacent 3' phosphate cannot be modified without severe loss of catalytic efficiency. The structural equivalence of key groups, conserved in the active sites of EcoRV, EcoRI, PvuII, and BamHI endonucleases, suggests that ligation of a catalytic divalent metal ion to this phosphate may occur in many type II restriction enzymes. Together with previous cocrystal structures, these data allow construction of a detailed model for the pretransition state configuration in EcoRV. This model features three divalent metal ions per active site and invokes assistance in the bond-making step by a conserved lysine, which stabilizes the attacking hydroxide ion nucleophile. |
==About this Structure== | ==About this Structure== | ||
| - | 1BSS 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:// | + | 1BSS 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=1BSS 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: Horton, N | + | [[Category: Horton, N C.]] |
| - | [[Category: Perona, J | + | [[Category: Perona, J J.]] |
[[Category: CA]] | [[Category: CA]] | ||
[[Category: complex (endonuclease ecorv/dna)]] | [[Category: complex (endonuclease ecorv/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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ECORV-T93A/DNA/CA2+
Overview
The 2.15-A resolution cocrystal structure of EcoRV endonuclease mutant T93A complexed with DNA and Ca2+ ions reveals two divalent metals bound in one of the active sites. One of these metals is ligated through an inner-sphere water molecule to the phosphate group located 3' to the scissile phosphate. A second inner-sphere water on this metal is positioned approximately in-line for attack on the scissile phosphate. This structure corroborates the observation that the pro-SP phosphoryl oxygen on the adjacent 3' phosphate cannot be modified without severe loss of catalytic efficiency. The structural equivalence of key groups, conserved in the active sites of EcoRV, EcoRI, PvuII, and BamHI endonucleases, suggests that ligation of a catalytic divalent metal ion to this phosphate may occur in many type II restriction enzymes. Together with previous cocrystal structures, these data allow construction of a detailed model for the pretransition state configuration in EcoRV. This model features three divalent metal ions per active site and invokes assistance in the bond-making step by a conserved lysine, which stabilizes the attacking hydroxide ion nucleophile.
About this Structure
1BSS 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
Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases., Horton NC, Newberry KJ, Perona JJ, Proc Natl Acad Sci U S A. 1998 Nov 10;95(23):13489-94. PMID:9811827
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