1f0o: Difference between revisions
No edit summary |
No edit summary |
||
| Line 4: | Line 4: | ||
|PDB= 1f0o |SIZE=350|CAPTION= <scene name='initialview01'>1f0o</scene>, resolution 2.5Å | |PDB= 1f0o |SIZE=350|CAPTION= <scene name='initialview01'>1f0o</scene>, resolution 2.5Å | ||
|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=[[1eyu|1EYU]], [[3pyi|3PYI]], [[2pyi|2PYI]], [[1pvi|1PVI]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f0o OCA], [http://www.ebi.ac.uk/pdbsum/1f0o PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1f0o RCSB]</span> | |||
}} | }} | ||
| Line 25: | Line 28: | ||
[[Category: Cheng, X.]] | [[Category: Cheng, X.]] | ||
[[Category: Horton, J R.]] | [[Category: Horton, J R.]] | ||
[[Category: catalytic metal visualization]] | [[Category: catalytic metal visualization]] | ||
[[Category: endonuclease type ii]] | [[Category: endonuclease type ii]] | ||
| Line 31: | Line 33: | ||
[[Category: restriction enzyme]] | [[Category: restriction enzyme]] | ||
''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 20:13:26 2008'' | ||
Revision as of 20:13, 30 March 2008
| |||||||
| , resolution 2.5Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Activity: | Type II site-specific deoxyribonuclease, with EC number 3.1.21.4 | ||||||
| Related: | 1EYU, 3PYI, 2PYI, 1PVI
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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. 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
Page seeded by OCA on Sun Mar 30 20:13:26 2008