2sns
From Proteopedia
(New page: 200px<br /><applet load="2sns" size="450" color="white" frame="true" align="right" spinBox="true" caption="2sns, resolution 1.5Å" /> '''STAPHYLOCOCCAL NUCLEA...) |
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| - | [[Image:2sns.jpg|left|200px]]<br /><applet load="2sns" size=" | + | [[Image:2sns.jpg|left|200px]]<br /><applet load="2sns" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="2sns, resolution 1.5Å" /> | caption="2sns, resolution 1.5Å" /> | ||
'''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'''<br /> | '''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'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The structure of the staphylococcal nuclease (EC 3.1.4.7)-thymidine | + | 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== | ==About this Structure== | ||
| - | 2SNS 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]. This structure | + | 2SNS 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]. This structure supersedes the now removed PDB entry 1SNS. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2SNS OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Staphylococcus aureus]] | [[Category: Staphylococcus aureus]] | ||
| - | [[Category: Cotton, F | + | [[Category: Cotton, F A.]] |
| - | [[Category: Hazenjunior, E | + | [[Category: Hazenjunior, E E.]] |
| - | [[Category: Legg, M | + | [[Category: Legg, M 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 18:49:16 2008'' |
Revision as of 16:49, 21 February 2008
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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 with and as ligands. This structure supersedes the now removed PDB entry 1SNS. Active as Hydrolase, with EC number 3.1.33.1 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
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