1tw8: Difference between revisions
New page: left|200px<br /><applet load="1tw8" size="450" color="white" frame="true" align="right" spinBox="true" caption="1tw8, resolution 2.8Å" /> '''HincII bound to Ca2+ ... |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Image:1tw8.gif|left|200px]]<br /><applet load="1tw8" size=" | [[Image:1tw8.gif|left|200px]]<br /><applet load="1tw8" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1tw8, resolution 2.8Å" /> | caption="1tw8, resolution 2.8Å" /> | ||
'''HincII bound to Ca2+ and cognate DNA GTCGAC'''<br /> | '''HincII bound to Ca2+ and cognate DNA GTCGAC'''<br /> | ||
==Overview== | ==Overview== | ||
The 2.8 A crystal structure of the type II restriction endonuclease HincII | The 2.8 A crystal structure of the type II restriction endonuclease HincII bound to Ca(2+) and cognate DNA containing GTCGAC is presented. The DNA is uncleaved, and one calcium ion is bound per active site, in a position previously described as site I in the related blunt cutting type II restriction endonuclease EcoRV [Horton, N. C., Newberry, K. J., and Perona, J. J. (1998) Proc. Natl. Acad. Sci. U.S.A. 95 (23), 13489-13494], as well as that found in other related enzymes. Unlike the site I metal in EcoRV, but similar to that of PvuII, NgoMIV, BamHI, BglII, and BglI, the observed calcium cation is directly ligated to the pro-S(p) oxygen of the scissile phosphate. A calcium ion-ligated water molecule is well positioned to act as the nucleophile in the phosphodiester bond cleavage reaction, and is within hydrogen bonding distance of the conserved active site lysine (Lys 129), as well as the pro-R(p) oxygen of the phosphate group 3' of the scissile phosphate, suggesting possible roles for these groups in the catalytic mechanism. Kinetic data consistent with an important role for the 3'-phosphate group in DNA cleavage by HincII are presented. The previously observed sodium ion [Horton, N. C., Dorner, L. F., and Perona, J. J. (2002) Nat. Struct. Biol. 9, 42-47] persists in the active sites of the Ca(2+)-bound structure; however, kinetic data show little effect on the single-turnover rate of DNA cleavage in the absence of Na(+) ions. | ||
==About this Structure== | ==About this Structure== | ||
1TW8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae] with CA and NA as [http://en.wikipedia.org/wiki/ligands ligands]. 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:// | 1TW8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae] with <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=NA:'>NA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. 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=1TW8 OCA]. | ||
==Reference== | ==Reference== | ||
| Line 15: | Line 15: | ||
[[Category: Type II site-specific deoxyribonuclease]] | [[Category: Type II site-specific deoxyribonuclease]] | ||
[[Category: Etzkorn, C.]] | [[Category: Etzkorn, C.]] | ||
[[Category: Horton, N | [[Category: Horton, N C.]] | ||
[[Category: CA]] | [[Category: CA]] | ||
[[Category: NA]] | [[Category: NA]] | ||
[[Category: restriction endonuclease]] | [[Category: restriction endonuclease]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:18:01 2008'' | ||
Revision as of 16:18, 21 February 2008
|
HincII bound to Ca2+ and cognate DNA GTCGAC
OverviewOverview
The 2.8 A crystal structure of the type II restriction endonuclease HincII bound to Ca(2+) and cognate DNA containing GTCGAC is presented. The DNA is uncleaved, and one calcium ion is bound per active site, in a position previously described as site I in the related blunt cutting type II restriction endonuclease EcoRV [Horton, N. C., Newberry, K. J., and Perona, J. J. (1998) Proc. Natl. Acad. Sci. U.S.A. 95 (23), 13489-13494], as well as that found in other related enzymes. Unlike the site I metal in EcoRV, but similar to that of PvuII, NgoMIV, BamHI, BglII, and BglI, the observed calcium cation is directly ligated to the pro-S(p) oxygen of the scissile phosphate. A calcium ion-ligated water molecule is well positioned to act as the nucleophile in the phosphodiester bond cleavage reaction, and is within hydrogen bonding distance of the conserved active site lysine (Lys 129), as well as the pro-R(p) oxygen of the phosphate group 3' of the scissile phosphate, suggesting possible roles for these groups in the catalytic mechanism. Kinetic data consistent with an important role for the 3'-phosphate group in DNA cleavage by HincII are presented. The previously observed sodium ion [Horton, N. C., Dorner, L. F., and Perona, J. J. (2002) Nat. Struct. Biol. 9, 42-47] persists in the active sites of the Ca(2+)-bound structure; however, kinetic data show little effect on the single-turnover rate of DNA cleavage in the absence of Na(+) ions.
About this StructureAbout this Structure
1TW8 is a Single protein structure of sequence from Haemophilus influenzae with and as ligands. Active as Type II site-specific deoxyribonuclease, with EC number 3.1.21.4 Full crystallographic information is available from OCA.
ReferenceReference
Ca2+ binding in the active site of HincII: implications for the catalytic mechanism., Etzkorn C, Horton NC, Biochemistry. 2004 Oct 26;43(42):13256-70. PMID:15491133
Page seeded by OCA on Thu Feb 21 15:18:01 2008