1snc
From Proteopedia
(New page: 200px<br /><applet load="1snc" size="450" color="white" frame="true" align="right" spinBox="true" caption="1snc, resolution 1.65Å" /> '''THE CRYSTAL STRUCTUR...) |
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| - | [[Image:1snc.gif|left|200px]]<br /><applet load="1snc" size=" | + | [[Image:1snc.gif|left|200px]]<br /><applet load="1snc" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1snc, resolution 1.65Å" /> | caption="1snc, resolution 1.65Å" /> | ||
'''THE CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF STAPHYLOCOCCAL NUCLEASE, CA2+, AND THE INHIBITOR PD*TP, REFINED AT 1.65 ANGSTROMS'''<br /> | '''THE CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF STAPHYLOCOCCAL NUCLEASE, CA2+, AND THE INHIBITOR PD*TP, REFINED AT 1.65 ANGSTROMS'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The structure of a complex of staphylococcal nuclease with Ca2+ and | + | The structure of a complex of staphylococcal nuclease with Ca2+ and deoxythymidine 3',5'-bisphosphate (pdTp) has been refined by stereochemically restrained least-squares minimization to a crystallographic R value of 0.161 at 1.65 A resolution. The estimated root-mean-square (rms) error in the coordinates is 0.16 A. The final model comprises 1082 protein atoms, one calcium ion, the pdTp molecule, and 82 solvent water molecules; it displays an rms deviation from ideality of 0.017 A for bond distances and 1.8 degrees for bond angles. The mean distance between corresponding alpha carbons in the refined and unrefined structures is 0.6 A; we observe small but significant differences between the refined and unrefined models in the turn between residues 27 and 30, the loop between residues 44 and 50, the first helix, and the extended strand between residues 112 and 117 which forms part of the active site binding pocket. The details of the calcium liganding and solvent structure in the active site are clearly shown in the final electron density map. The structure of the catalytic site is consistent with the mechanism that has been proposed for this enzyme. However, we note that two lysines from a symmetry-related molecule in the crystal lattice may play an important role in determining the geometry of inhibitor binding, and that only one of the two required calcium ions is observed in the crystal structure; thus, caution is advised in extrapolating from the structure of the complex of enzyme and inhibitor to that of enzyme and substrate. |
==About this Structure== | ==About this Structure== | ||
| - | 1SNC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus] with CA and THP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] Full crystallographic information is available from [http:// | + | 1SNC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus] with <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=THP:'>THP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SNC OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Staphylococcus aureus]] | [[Category: Staphylococcus aureus]] | ||
| - | [[Category: Lattman, E | + | [[Category: Lattman, E E.]] |
| - | [[Category: Loll, P | + | [[Category: Loll, P J.]] |
[[Category: CA]] | [[Category: CA]] | ||
[[Category: THP]] | [[Category: THP]] | ||
[[Category: hydrolase (phosphoric diester)]] | [[Category: hydrolase (phosphoric diester)]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:03:19 2008'' |
Revision as of 13:03, 21 February 2008
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THE CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF STAPHYLOCOCCAL NUCLEASE, CA2+, AND THE INHIBITOR PD*TP, REFINED AT 1.65 ANGSTROMS
Overview
The structure of a complex of staphylococcal nuclease with Ca2+ and deoxythymidine 3',5'-bisphosphate (pdTp) has been refined by stereochemically restrained least-squares minimization to a crystallographic R value of 0.161 at 1.65 A resolution. The estimated root-mean-square (rms) error in the coordinates is 0.16 A. The final model comprises 1082 protein atoms, one calcium ion, the pdTp molecule, and 82 solvent water molecules; it displays an rms deviation from ideality of 0.017 A for bond distances and 1.8 degrees for bond angles. The mean distance between corresponding alpha carbons in the refined and unrefined structures is 0.6 A; we observe small but significant differences between the refined and unrefined models in the turn between residues 27 and 30, the loop between residues 44 and 50, the first helix, and the extended strand between residues 112 and 117 which forms part of the active site binding pocket. The details of the calcium liganding and solvent structure in the active site are clearly shown in the final electron density map. The structure of the catalytic site is consistent with the mechanism that has been proposed for this enzyme. However, we note that two lysines from a symmetry-related molecule in the crystal lattice may play an important role in determining the geometry of inhibitor binding, and that only one of the two required calcium ions is observed in the crystal structure; thus, caution is advised in extrapolating from the structure of the complex of enzyme and inhibitor to that of enzyme and substrate.
About this Structure
1SNC is a Single protein structure of sequence from Staphylococcus aureus with and as ligands. Active as Micrococcal nuclease, with EC number 3.1.31.1 Full crystallographic information is available from OCA.
Reference
The crystal structure of the ternary complex of staphylococcal nuclease, Ca2+, and the inhibitor pdTp, refined at 1.65 A., Loll PJ, Lattman EE, Proteins. 1989;5(3):183-201. PMID:2780539
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