Crystal structure of Penicillium citrinum P1 nuclease at 2.8 A resolution.
P1 nuclease from Penicillium citrinum is a zinc dependent glyco-enzyme consisting of 270 amino acid residues which cleaves single-stranded RNA and DNA into 5'-mononucleotides. The X-ray structure of a tetragonal crystal form of the enzyme with two molecules per asymmetric unit has been solved at 3.3 and refined at 2.8 A resolution to a crystallographic R-factor of 21.6%. The current model consists of 269 amino acid residues, three Zn ions and two N-acetyl glucosamines per subunit. The enzyme is folded very similarly to phospholipase C from Bacillus cereus, with 56% of the structure displaying an alpha-helical conformation. The three Zn ions are located at the bottom of a cleft and appear to be rather inaccessible for any phosphate group in double-stranded RNA or DNA substrates. A crystal soaking experiment with a dinucleotide gives clear evidence for two mononucleotide binding sites separated by approximately 20 A. One site shows binding of the phosphate group to one of the zinc ions. At both sites there is a hydrophobic binding pocket for the base, but no direct interaction between the protein and the deoxyribose. A cleavage mechanism is proposed involving nucleophilic attack by a Zn activated water molecule.
Volbeda
A
A
European Molecular Biology Laboratory, Heidelberg, Germany.
Lahm
A
A
Sakiyama
F
F
Suck
D
D
D000117:Acetylglucosamine / Q000737:chemistry; D000595:Amino Acid Sequence; D001409:Bacillus cereus / Q000201:enzymology; D002264:Carboxylic Acids / Q000737:chemistry; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry; D005656:Fungal Proteins / Q000737:chemistry*; D006868:Hydrolysis; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010407:Penicillium / Q000201:enzymology*; D011487:Protein Conformation; D012313:RNA / Q000737:chemistry / Q000378:metabolism; D015719:Single-Strand Specific DNA and RNA Endonucleases / Q000737:chemistry*; D013379:Substrate Specificity; D014961:X-Ray Diffraction; D015032:Zinc / Q000502:physiology
D002264:Carboxylic Acids; D004268:DNA-Binding Proteins; D005656:Fungal Proteins; D012313:RNA; D004247:DNA; D015719:Single-Strand Specific DNA and RNA Endonucleases; D015032:Zinc; D000117:Acetylglucosamine