1bss
From Proteopedia
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|PDB= 1bss |SIZE=350|CAPTION= <scene name='initialview01'>1bss</scene>, resolution 2.15Å | |PDB= 1bss |SIZE=350|CAPTION= <scene name='initialview01'>1bss</scene>, resolution 2.15Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM ION'>CA</scene> | + | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</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] | + | |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> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1bss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bss OCA], [http://www.ebi.ac.uk/pdbsum/1bss PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1bss RCSB]</span> | ||
}} | }} | ||
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[[Category: Horton, N C.]] | [[Category: Horton, N C.]] | ||
[[Category: Perona, J J.]] | [[Category: Perona, J J.]] | ||
| - | [[Category: CA]] | ||
[[Category: complex (endonuclease ecorv/dna)]] | [[Category: complex (endonuclease ecorv/dna)]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:07:32 2008'' |
Revision as of 16:07, 30 March 2008
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| , resolution 2.15Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Activity: | Type II site-specific deoxyribonuclease, with EC number 3.1.21.4 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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. 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
Page seeded by OCA on Sun Mar 30 19:07:32 2008
