2sns
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 2sns |SIZE=350|CAPTION= <scene name='initialview01'>2sns</scene>, resolution 1.5Å | |PDB= 2sns |SIZE=350|CAPTION= <scene name='initialview01'>2sns</scene>, resolution 1.5Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=THP:THYMIDINE-3 | + | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=THP:THYMIDINE-3',5'-DIPHOSPHATE'>THP</scene> |
|ACTIVITY= [http://en.wikipedia.org/wiki/Hydrolase Hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.33.1 3.1.33.1] | |ACTIVITY= [http://en.wikipedia.org/wiki/Hydrolase Hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.33.1 3.1.33.1] | ||
|GENE= | |GENE= | ||
| Line 30: | Line 30: | ||
[[Category: hydrolase (phosphoric diester)]] | [[Category: hydrolase (phosphoric diester)]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 15:50:34 2008'' |
Revision as of 13:50, 23 March 2008
| |||||||
| , resolution 1.5Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | and | ||||||
| Activity: | Hydrolase, with EC number 3.1.33.1 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
STAPHYLOCOCCAL NUCLEASE. PROPOSED MECHANISM OF ACTION BASED ON STRUCTURE OF ENZYME-THYMIDINE 3(PRIME),5(PRIME)-BIPHOSPHATE-CALCIUM ION COMPLEX AT 1.5-ANGSTROMS RESOLUTION
Overview
The structure of the staphylococcal nuclease (EC 3.1.4.7)-thymidine 3',5'-bisphosphate-Ca(2+) (enzyme-inhibitor) complex has been extended to 1.5-A resolution by using much additional data and a phase refinement scheme based on an electron-density map modification procedure. By correlating this structure with the known properties of the enzyme, a mechanism of action is proposed that involves nucleophilic attack on phosphorus by a water molecule, which is bound to Glu-43, in line with the 5'-CH(2)O(H) leaving group. The carboxylate of Glu-43 promotes this attack by acting as a general base for the abstraction of a proton from the attacking water molecule. Nucleophilic attack is further facilitated by polarization of the phosphodiester by an ionic interaction between a Ca(2+) ion and a phosphate oxygen atom and by four hydrogen bonds to phosphate oxygen atoms from guanidinium ions of Arg-35 and Arg-87. These interactions may also catalyze the reaction by lowering the energy of a trigonal bipyramidal transition state. The hydrolysis of nucleic acid substrate proceeds by cleavage of the 5'-P-O bond to yield a free 5'-hydroxyl group and a terminal, 3'-phosphate monoester group. In the inhibitor complex the only general acid group found in a position to donate a proton to the leaving 5'-oxygen is the guanidinium ion of Arg-87. Alternative proton donors, presently lacking direct structural support, could be the phenolic hydroxyl group of Tyr-113 or a water molecule. The precision and rigidity of the location of the reactants at the active site and the probable dual binding and catalytic roles of the guanidinium ions of Arg-35 and Arg-87 are especially noteworthy.
About this Structure
2SNS is a Single protein structure of sequence from Staphylococcus aureus. This structure supersedes the now removed PDB entry 1SNS. Full crystallographic information is available from OCA.
Reference
Staphylococcal nuclease: proposed mechanism of action based on structure of enzyme-thymidine 3',5'-bisphosphate-calcium ion complex at 1.5-A resolution., Cotton FA, Hazen EE Jr, Legg MJ, Proc Natl Acad Sci U S A. 1979 Jun;76(6):2551-5. PMID:288045
Page seeded by OCA on Sun Mar 23 15:50:34 2008
