1ak0
From Proteopedia
(New page: 200px<br /><applet load="1ak0" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ak0, resolution 1.8Å" /> '''P1 NUCLEASE IN COMPLE...) |
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| - | [[Image:1ak0.gif|left|200px]]<br /><applet load="1ak0" size=" | + | [[Image:1ak0.gif|left|200px]]<br /><applet load="1ak0" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1ak0, resolution 1.8Å" /> | caption="1ak0, resolution 1.8Å" /> | ||
'''P1 NUCLEASE IN COMPLEX WITH A SUBSTRATE ANALOG'''<br /> | '''P1 NUCLEASE IN COMPLEX WITH A SUBSTRATE ANALOG'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The reaction mechanism of nuclease P1 from Penicillium citrinum has been | + | The reaction mechanism of nuclease P1 from Penicillium citrinum has been investigated using single-stranded dithiophosphorylated di-, tetra-, and hexanucleotides as substrate analogs. The complexes crystallize in tetragonal and orthorhombic space groups and have been solved by molecular replacement. The high resolution structures give a clear picture of base recognition by P1 nuclease at its two nucleotide-binding sites, especially the 1.8 A structure of a P1-tetranucleotide complex which can be considered a P1-product complex. The observed binding modes are in agreement with a catalytic mechanism where the two closely spaced zinc ions activate the attacking water while the third, more exposed zinc ion stabilizes the leaving 03' oxyanion. Stacking as well as hydrogen bonding interactions with the base 5' to the cleaved phosphodiester bond are important elements of substrate binding and recognition. Modelling of a productive P1-substrate complex based on the solved structures suggests steric hindrance as the likely reason for the resistance of Rp-phosphorothioates and phosphorodithioates. Differences with the highly homologous nuclease S1 from Aspergillus oryzae are discussed. |
==About this Structure== | ==About this Structure== | ||
| - | 1AK0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Penicillium_citrinum Penicillium citrinum] with NAG, ZN and ADS as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Aspergillus_nuclease_S(1) Aspergillus nuclease S(1)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.30.1 3.1.30.1] Full crystallographic information is available from [http:// | + | 1AK0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Penicillium_citrinum Penicillium citrinum] with <scene name='pdbligand=NAG:'>NAG</scene>, <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=ADS:'>ADS</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Aspergillus_nuclease_S(1) Aspergillus nuclease S(1)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.30.1 3.1.30.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AK0 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: thiophosphorylated oligonucleotides]] | [[Category: thiophosphorylated oligonucleotides]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:45:22 2008'' |
Revision as of 09:45, 21 February 2008
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P1 NUCLEASE IN COMPLEX WITH A SUBSTRATE ANALOG
Overview
The reaction mechanism of nuclease P1 from Penicillium citrinum has been investigated using single-stranded dithiophosphorylated di-, tetra-, and hexanucleotides as substrate analogs. The complexes crystallize in tetragonal and orthorhombic space groups and have been solved by molecular replacement. The high resolution structures give a clear picture of base recognition by P1 nuclease at its two nucleotide-binding sites, especially the 1.8 A structure of a P1-tetranucleotide complex which can be considered a P1-product complex. The observed binding modes are in agreement with a catalytic mechanism where the two closely spaced zinc ions activate the attacking water while the third, more exposed zinc ion stabilizes the leaving 03' oxyanion. Stacking as well as hydrogen bonding interactions with the base 5' to the cleaved phosphodiester bond are important elements of substrate binding and recognition. Modelling of a productive P1-substrate complex based on the solved structures suggests steric hindrance as the likely reason for the resistance of Rp-phosphorothioates and phosphorodithioates. Differences with the highly homologous nuclease S1 from Aspergillus oryzae are discussed.
About this Structure
1AK0 is a Single protein structure of sequence from Penicillium citrinum with , and as ligands. Active as Aspergillus nuclease S(1), with EC number 3.1.30.1 Full crystallographic information is available from OCA.
Reference
Recognition of single-stranded DNA by nuclease P1: high resolution crystal structures of complexes with substrate analogs., Romier C, Dominguez R, Lahm A, Dahl O, Suck D, Proteins. 1998 Sep 1;32(4):414-24. PMID:9726413
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