3dh2 | pdb_00003dh2

Crystal structure of ribonuclease Sa2 with guanosine-3'-cyclophosphate prepared by cocrystallization

spinqualitylabelsall models 3dh2, resolution 2.25Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3dh2 is a 4 chain structure with sequence from Kitasatospora aureofaciens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.25Å Ligands: 3GP, BGC, SO4 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function Q53752_KITAU Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed Although the mechanism of RNA cleavage by RNases has been studied for many years, there remain aspects that have not yet been fully clarified. We have solved the crystal structures of RNase Sa2 in the apo form and in complexes with mononucleotides. These structures provide more details about the mechanism of RNA cleavage by RNase Sa2. In addition to Glu56 and His86, which are the principal catalytic residues, an important role in the first reaction step of RNA cleavage also seems to be played by Arg67 and Arg71, which are located in the phosphate-binding site and form hydrogen bonds with the oxygens of the phosphate group of the mononucleotides. Their positive charge very likely causes polarization of the bonds between the oxygens and the phosphorus atom, leading to electron deficiency on the phosphorus atom and facilitating nucleophilic attack by O2' of the ribose on the phosphorus atom, leading to cyclophosphate formation. The negatively charged Glu56 is in position to attract the proton from O2' of the ribose. Extended molecular docking of mononucleotides, dinucleotides and trinucleotides into the active site of the enzyme allowed us to better understand the guanosine specificity of RNase Sa2 and to predict possible binding subsites for the downstream base and ribose of the second and third nucleotides. Structure of RNase Sa2 complexes with mononucleotides--new aspects of catalytic reaction and substrate recognition.,Bauerova-Hlinkova V, Dvorsky R, Perecko D, Povazanec F, Sevcik J FEBS J. 2009 Aug;276(15):4156-68. Epub 2009 Jun 25. PMID:19558492 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Ribonuclease 3D structures

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