1f0o: Difference between revisions
New page: left|200px<br /><applet load="1f0o" size="450" color="white" frame="true" align="right" spinBox="true" caption="1f0o, resolution 2.5Å" /> '''PVUII ENDONUCLEASE/CO... |
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[[Image:1f0o.gif|left|200px]]<br /><applet load="1f0o" size=" | [[Image:1f0o.gif|left|200px]]<br /><applet load="1f0o" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1f0o, resolution 2.5Å" /> | caption="1f0o, resolution 2.5Å" /> | ||
'''PVUII ENDONUCLEASE/COGNATE DNA COMPLEX (GLUTARALDEHYDE-CROSSLINKED CRYSTAL) AT PH 7.5 WITH TWO CALCIUM IONS AT EACH ACTIVE SITE'''<br /> | '''PVUII ENDONUCLEASE/COGNATE DNA COMPLEX (GLUTARALDEHYDE-CROSSLINKED CRYSTAL) AT PH 7.5 WITH TWO CALCIUM IONS AT EACH ACTIVE SITE'''<br /> | ||
==Overview== | ==Overview== | ||
Restriction endonucleases differ in their use of metal cofactors despite | Restriction endonucleases differ in their use of metal cofactors despite having remarkably similar folds for their catalytic regions. To explore this, we have characterized the interaction of endonuclease PvuII with the catalytically incompetent cation Ca(2+). The structure of a glutaraldehyde-crosslinked crystal of the endonuclease PvuII-DNA complex, determined in the presence of Ca(2+) at a pH of approximately 6.5, supports a two-metal mechanism of DNA cleavage by PvuII. The first Ca(2+) position matches that found in all structurally examined endonucleases, while the second position is similar to that of EcoRV but is distinct from that of BamHI and BglI. The location of the second metal in PvuII, unlike that in BamHI/BglI, permits no direct interaction between the second metal and the O3' oxygen leaving group. However, the interactions between the DNA scissile phosphate and the metals, the first metal and the attacking water, and the attacking water and DNA are the same in PvuII as they are in the two-metal models of BamHI and BglI, but are distinct from the proposed three-metal or the two-metal models of EcoRV. | ||
==About this Structure== | ==About this Structure== | ||
1F0O is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Proteus_vulgaris Proteus vulgaris] 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:// | 1F0O is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Proteus_vulgaris Proteus vulgaris] 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=1F0O OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Type II site-specific deoxyribonuclease]] | [[Category: Type II site-specific deoxyribonuclease]] | ||
[[Category: Cheng, X.]] | [[Category: Cheng, X.]] | ||
[[Category: Horton, J | [[Category: Horton, J R.]] | ||
[[Category: CA]] | [[Category: CA]] | ||
[[Category: catalytic metal visualization]] | [[Category: catalytic metal visualization]] | ||
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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 12:33:37 2008'' | ||
Revision as of 13:33, 21 February 2008
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PVUII ENDONUCLEASE/COGNATE DNA COMPLEX (GLUTARALDEHYDE-CROSSLINKED CRYSTAL) AT PH 7.5 WITH TWO CALCIUM IONS AT EACH ACTIVE SITE
OverviewOverview
Restriction endonucleases differ in their use of metal cofactors despite having remarkably similar folds for their catalytic regions. To explore this, we have characterized the interaction of endonuclease PvuII with the catalytically incompetent cation Ca(2+). The structure of a glutaraldehyde-crosslinked crystal of the endonuclease PvuII-DNA complex, determined in the presence of Ca(2+) at a pH of approximately 6.5, supports a two-metal mechanism of DNA cleavage by PvuII. The first Ca(2+) position matches that found in all structurally examined endonucleases, while the second position is similar to that of EcoRV but is distinct from that of BamHI and BglI. The location of the second metal in PvuII, unlike that in BamHI/BglI, permits no direct interaction between the second metal and the O3' oxygen leaving group. However, the interactions between the DNA scissile phosphate and the metals, the first metal and the attacking water, and the attacking water and DNA are the same in PvuII as they are in the two-metal models of BamHI and BglI, but are distinct from the proposed three-metal or the two-metal models of EcoRV.
About this StructureAbout this Structure
1F0O is a Single protein structure of sequence from Proteus vulgaris with as ligand. Active as Type II site-specific deoxyribonuclease, with EC number 3.1.21.4 Full crystallographic information is available from OCA.
ReferenceReference
PvuII endonuclease contains two calcium ions in active sites., Horton JR, Cheng X, J Mol Biol. 2000 Jul 28;300(5):1049-56. PMID:10903853
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