2b0d: Difference between revisions
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[[Image:2b0d.gif|left|200px]] | [[Image:2b0d.gif|left|200px]] | ||
'''EcoRV Restriction Endonuclease/GAATTC/Ca2+''' | {{Structure | ||
|PDB= 2b0d |SIZE=350|CAPTION= <scene name='initialview01'>2b0d</scene>, resolution 2.0Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=CA:CALCIUM ION'>CA</scene> | |||
|ACTIVITY= [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] | |||
|GENE= ecoRVR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | |||
}} | |||
'''EcoRV Restriction Endonuclease/GAATTC/Ca2+''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2B0D is a [ | 2B0D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B0D OCA]. | ||
==Reference== | ==Reference== | ||
Non-cognate enzyme-DNA complex: structural and kinetic analysis of EcoRV endonuclease bound to the EcoRI recognition site GAATTC., Hiller DA, Rodriguez AM, Perona JJ, J Mol Biol. 2005 Nov 18;354(1):121-36. Epub 2005 Oct 3. PMID:[http:// | Non-cognate enzyme-DNA complex: structural and kinetic analysis of EcoRV endonuclease bound to the EcoRI recognition site GAATTC., Hiller DA, Rodriguez AM, Perona JJ, J Mol Biol. 2005 Nov 18;354(1):121-36. Epub 2005 Oct 3. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16236314 16236314] | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: substrate specificity]] | [[Category: substrate specificity]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:56:04 2008'' | ||
Revision as of 16:56, 20 March 2008
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| , resolution 2.0Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Gene: | ecoRVR (Escherichia coli) | ||||||
| Activity: | Type II site-specific deoxyribonuclease, with EC number 3.1.21.4 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
EcoRV Restriction Endonuclease/GAATTC/Ca2+
OverviewOverview
The crystal structure of EcoRV endonuclease bound to non-cognate DNA at 2.0 angstroms resolution shows that very small structural adaptations are sufficient to ensure the extreme sequence specificity characteristic of restriction enzymes. EcoRV bends its specific GATATC site sharply by 50 degrees into the major groove at the center TA step, generating unusual base-base interactions along each individual DNA strand. In the symmetric non-cognate complex bound to GAATTC, the center step bend is relaxed to avoid steric hindrance caused by the different placement of the exocyclic thymine methyl groups. The decreased base-pair unstacking in turn leads to small conformational rearrangements in the sugar-phosphate backbone, sufficient to destabilize binding of crucial divalent metal ions in the active site. A second crystal structure of EcoRV bound to the base-analog GAAUTC site shows that the 50 degrees center-step bend of the DNA is restored. However, while divalent metals bind at high occupancy in this structure, one metal ion shifts away from binding at the scissile DNA phosphate to a position near the 3'-adjacent phosphate group. This may explain why the 10(4)-fold attenuated cleavage efficiency toward GAATTC is reconstituted by less than tenfold toward GAAUTC. Examination of DNA binding and bending by equilibrium and stopped-flow florescence quenching and fluorescence resonance energy transfer (FRET) methods demonstrates that the capacity of EcoRV to bend the GAATTC non-cognate site is severely limited, but that full bending of GAAUTC is achieved at only a threefold reduced rate compared with the cognate complex. Together, the structural and biochemical data demonstrate the existence of distinct mechanisms for ensuring specificity at the bending and catalytic steps, respectively. The limited conformational rearrangements observed in the EcoRV non-cognate complex provide a sharp contrast to the extensive structural changes found in a non-cognate BamHI-DNA crystal structure, thus demonstrating a diversity of mechanisms by which restriction enzymes are able to achieve specificity.
About this StructureAbout this Structure
2B0D is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
ReferenceReference
Non-cognate enzyme-DNA complex: structural and kinetic analysis of EcoRV endonuclease bound to the EcoRI recognition site GAATTC., Hiller DA, Rodriguez AM, Perona JJ, J Mol Biol. 2005 Nov 18;354(1):121-36. Epub 2005 Oct 3. PMID:16236314
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