1qae

THE ACTIVE SITE OF SERRATIA ENDONUCLEASE CONTAINS A CONSERVED MAGNESIUM-WATER CLUSTER

spinqualitylabelsall models 1qae, resolution 2.05Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 1qae is a 2 chain structure with sequence from "bacillus_marcescens"_(bizio_1823)_trevisan_in_de_toni_and_trevisan_1889 "bacillus marcescens" (bizio 1823) trevisan in de toni and trevisan 1889. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: MG Activity: Serratia marcescens nuclease, with EC number 3.1.30.2 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [NUCA_SERMA] Catalyzes the hydrolysis of both DNA and RNA, double- or single-stranded, at the 3'position of the phosphodiester bond to produce 5'-phosphorylated mono-, di-, tri- and tetranucleotides. DNA is a slightly better substrate than RNA. 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 Serratia endonuclease is an important member of a class of magnesium dependent nucleases that are widely distributed in nature. Here, we describe the location and geometry of a magnesium-water cluster within the active site of this enzyme. The sole protein ligand of the magnesium atom is Asn119; this metal ion is also associated with five water molecules to complete an octahedral coordination complex. These water molecules are very well ordered and there is no evidence of rotational disorder or motion. Glu127 and His89 are located nearby and each is hydrogen bonded to water molecules in the coordination sphere. Asp86 is not chelated to the magnesium or its surrounding water molecules. Results of kinetics and site-specific mutagenesis experiments suggest that this metal-water cluster contains the catalytic metal ion of this enzyme. All residues which hydrogen bond to the water molecules that coordinate the magnesium atom are conserved in nucleases homologous to Serratia endonuclease, suggesting that the water cluster is a conserved feature of this family of enzymes. We offer a detailed structural comparison to one other nuclease, the homing endonuclease I-PpoI, that has recently been shown, in spite of a lack of sequence homology, to share a similar active site geometry to Serratia endonuclease. Evidence from both of these structures suggests that the magnesium of Serratia nuclease participates in catalysis via an inner sphere mechanism. The active site of Serratia endonuclease contains a conserved magnesium-water cluster.,Miller MD, Cai J, Krause KL J Mol Biol. 1999 May 21;288(5):975-87. PMID:10329193 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Endonuclease 3D structures

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