1AK0

P1 NUCLEASE IN COMPLEX WITH A SUBSTRATE ANALOG

Summary for 1AK0

• Entry DOI: 10.2210/pdb1ak0/pdb
• Descriptor: P1 NUCLEASE, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (7 entities in total)
• Functional Keywords: endonuclease, p1 nuclease, reaction mechanism, thiophosphorylated oligonucleotides, glycosylated protein
• Biological source: Penicillium citrinum
• Cellular location: Secreted: P24289
• Total number of polymer chains: 1
• Total formula weight: 31821.85

Authors

Romier, C.,Suck, D. (deposition date: 1997-05-28, release date: 1997-12-03, Last modification date: 2024-10-23)

Primary citation

Romier, C.,Dominguez, R.,Lahm, A.,Dahl, O.,Suck, D.
Recognition of single-stranded DNA by nuclease P1: high resolution crystal structures of complexes with substrate analogs.
Proteins, 32:414-424, 1998

PubMed Abstract: 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.

PubMed: 9726413
DOI: 10.1002/(SICI)1097-0134(19980901)32:4<414::AID-PROT2>3.3.CO;2-5

Experimental method

X-RAY DIFFRACTION (1.8 Å)