2cbn

Crystal structure of ZipD from Escherichia coli

spinqualitylabelsall models 2cbn, resolution 2.90Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2cbn is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.9Å Ligands: ZN Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function RBN_ECOLI Zinc phosphodiesterase, which has both exoribonuclease and endoribonuclease activities, depending on the nature of the substrate and of the added divalent cation, and on its 3'-terminal structure. Can process the 3' termini of both CCA-less and CCA-containing tRNA precursors. CCA-less tRNAs are cleaved endonucleolytically after the discriminator base, whereas residues following the CCA sequence can be removed exonucleolytically or endonucleolytically in CCA-containing molecules. Does not remove the CCA sequence. May also be involved in the degradation of mRNAs. In vitro, hydrolyzes bis(p-nitrophenyl)phosphate and thymidine-5'-p-nitrophenyl phosphate. 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 The elaC gene product from Escherichia coli, ZiPD, is a 3' tRNA-processing endonuclease belonging to the tRNase Z family of enzymes that have been identified in a wide variety of organisms. In contrast to the elaC homologue from Bacillus subtilis, E. coli elaC is not essential for viability, and although both enzymes process only precursor tRNA (pre-tRNA) lacking a CCA triplet at the 3' end in vitro, the physiological role of ZiPD remains enigmatic because all pre-tRNA species in E. coli are transcribed with the CCA triplet. We present the first crystal structure of ZiPD determined by multiple anomalous diffraction at a resolution of 2.9 A. This structure shares many features with the tRNase Z enzymes from B. subtilis and Thermotoga maritima, but there are distinct differences in metal binding and overall domain organization. Unlike the previously described homologous structures, ZiPD dimers display crystallographic symmetry and fully loaded metal sites. The ZiPD exosite is similar to that of the B. subtilis enzyme structurally, but its position with respect to the protein core differs substantially, illustrating its ability to act as a clamp in binding tRNA. Furthermore, the ZiPD crystal structure presented here provides insight into the enzyme's cooperativity and assists the ongoing attempt to elucidate the physiological function of this protein. The crystal structure of the zinc phosphodiesterase from Escherichia coli provides insight into function and cooperativity of tRNase Z-family proteins.,Kostelecky B, Pohl E, Vogel A, Schilling O, Meyer-Klaucke W J Bacteriol. 2006 Feb;188(4):1607-14. PMID:16452444 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Ribonuclease 3D structures

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