1ak0: Difference between revisions
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|PDB= 1ak0 |SIZE=350|CAPTION= <scene name='initialview01'>1ak0</scene>, resolution 1.8Å | |PDB= 1ak0 |SIZE=350|CAPTION= <scene name='initialview01'>1ak0</scene>, resolution 1.8Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=ADS:ADENOSINE-5'-(DITHIO)PHOSPHATE'>ADS</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=THS:THYMIDINE-5'-(DITHIO)PHOSPHATE'>THS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> | ||
|ACTIVITY= [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] | |ACTIVITY= <span class='plainlinks'>[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] </span> | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ak0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ak0 OCA], [http://www.ebi.ac.uk/pdbsum/1ak0 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ak0 RCSB]</span> | |||
}} | }} | ||
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[[Category: Romier, C.]] | [[Category: Romier, C.]] | ||
[[Category: Suck, D.]] | [[Category: Suck, D.]] | ||
[[Category: endonuclease]] | [[Category: endonuclease]] | ||
[[Category: glycosylated protein]] | [[Category: glycosylated protein]] | ||
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[[Category: thiophosphorylated oligonucleotide]] | [[Category: thiophosphorylated oligonucleotide]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:41:56 2008'' | ||
Revision as of 18:42, 30 March 2008
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| , resolution 1.8Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Activity: | Aspergillus nuclease S(1), with EC number 3.1.30.1 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
P1 NUCLEASE IN COMPLEX WITH A SUBSTRATE ANALOG
OverviewOverview
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 StructureAbout this Structure
1AK0 is a Single protein structure of sequence from Penicillium citrinum. Full crystallographic information is available from OCA.
ReferenceReference
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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