1xhv
From Proteopedia
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|PDB= 1xhv |SIZE=350|CAPTION= <scene name='initialview01'>1xhv</scene>, resolution 2.5Å | |PDB= 1xhv |SIZE=350|CAPTION= <scene name='initialview01'>1xhv</scene>, resolution 2.5Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=MN:MANGANESE (II) ION'>MN</scene> | + | |LIGAND= <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>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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= hincIIR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 Haemophilus influenzae]) | |GENE= hincIIR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 Haemophilus influenzae]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1kc6|1KC6]], [[1tw8|1TW8]], [[1xhu|1XHU]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xhv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xhv OCA], [http://www.ebi.ac.uk/pdbsum/1xhv PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1xhv RCSB]</span> | ||
}} | }} | ||
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[[Category: Etzkorn, C.]] | [[Category: Etzkorn, C.]] | ||
[[Category: Horton, N C.]] | [[Category: Horton, N C.]] | ||
| - | [[Category: MN]] | ||
[[Category: phosphoryl transfer]] | [[Category: phosphoryl transfer]] | ||
[[Category: restriction endonuclease]] | [[Category: restriction endonuclease]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:49:55 2008'' |
Revision as of 21:49, 30 March 2008
| |||||||
| , resolution 2.5Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Gene: | hincIIR (Haemophilus influenzae) | ||||||
| Activity: | Type II site-specific deoxyribonuclease, with EC number 3.1.21.4 | ||||||
| Related: | 1KC6, 1TW8, 1XHU
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
HincII bound to cleaved cognate DNA GTCGAC and Mn2+
Overview
The three-dimensional X-ray crystal structures of HincII bound to cognate DNA containing GTCGAC and Mn(2+) or Mg(2+), at 2.50A and 2.95A resolution, respectively, are presented. In both structures, the DNA is found cleaved, and the positions of the active-site groups, cleaved phosphate group, and 3' oxygen atom of the leaving group are in very similar positions. Two highly occupied Mn(2+) positions are found in each active site of the four crystallographically independent subunit copies in the HincII/DNA/Mn(2+) structure. The manganese ion closest to the previously identified single Ca(2+) position of HincII is shifted 1.7A and has lost direct ligation to the active-site aspartate residue, Asp127. A Mn(2+)-ligated water molecule in a position analogous to that seen in the HincII/DNA/Ca(2+) structure, and proposed to be the attacking nucleophile, is beyond hydrogen bonding distance from the active-site lysine residue, Lys129, but remains within hydrogen bonding distance from the proRp oxygen atom of the phosphate group 3' to the scissile phosphate group. In addition, the position of the cleaved phosphate group is on the opposite side of the axis connecting the two metal ions relative to that found in the BamHI/product DNA/Mn(2+) structure. Mechanistic implications are discussed, and a model for the two-metal-ion mechanism of DNA cleavage by HincII is proposed.
About this Structure
1XHV is a Single protein structure of sequence from Haemophilus influenzae. Full crystallographic information is available from OCA.
Reference
Mechanistic insights from the structures of HincII bound to cognate DNA cleaved from addition of Mg2+ and Mn2+., Etzkorn C, Horton NC, J Mol Biol. 2004 Oct 29;343(4):833-49. PMID:15476804
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