2kmn

Solution structure of peptide deformylase complexed with actinonin

spinqualitylabelsall models 2kmn, 20 NMR models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2kmn is a 1 chain structure with sequence from Ecoli. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: BB2, ZN Gene: def, fms, b3287, JW3248 (ECOLI) Activity: Peptide deformylase, with EC number 3.5.1.88 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [DEF_ECOLI] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions.[HAMAP-Rule:MF_00163] 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 Peptide deformylase (PDF) is an enzyme that is responsible for removing the formyl group from nascently synthesized polypeptides in bacteria, attracting much attention as a potential target for novel antibacterial agents. Efforts to develop potent inhibitors of the enzyme have progressed on the basis of classical medicinal chemistry, combinatorial chemistry, and structural approaches, yet the validity of PDF as an antibacterial target hangs, in part, on the ability of inhibitors to selectively target this enzyme in favor of structurally related metallohydrolases. We have used (15)N NMR spectroscopy and isothermal titration calorimetry to investigate the high-affinity interaction of EcPDF with actinonin, a naturally occurring potent EcPDF inhibitor. Backbone amide chemical shifts, residual dipolar couplings, hydrogen-deuterium exchange, and (15)N relaxation reveal structural and dynamic effects of ligand binding in the immediate vicinity of the ligand-binding site as well as at remote sites. A comparison of the crystal structures of free and actinonin-bound EcPDF with the solution data suggests that most of the consequences of the ligand binding to the protein are lost or obscured during crystallization. The results of these studies improve our understanding of the thermodynamic global minimum and have important implications for structure-based drug design. Ligand-induced changes in the structure and dynamics of Escherichia coli peptide deformylase.,Amero CD, Byerly DW, McElroy CA, Simmons A, Foster MP Biochemistry. 2009 Aug 18;48(32):7595-607. PMID:19627112 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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