3pn3

Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) in complex with inhibitor 21

spinqualitylabelsall models 3pn3, resolution 1.30Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3pn3 is a 2 chain structure with sequence from Arath. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: PN3, ZN Related: 3pn2, 3pn6, 3pn4, 3pn5, 3m6o, 3o3j, 3m6q, 3m6r Gene: DEF2, PDF1B (ARATH) Activity: Peptide deformylase, with EC number 3.5.1.88 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [DEF1B_ARATH] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Has a preferred substrate specificity towards the photosystem II (PS II) D1 polypeptide. Publication Abstract from PubMed For several decades, molecular recognition has been considered one of the most fundamental processes in biochemistry. For enzymes, substrate binding is often coupled to conformational changes that alter the local environment of the active site to align the reactive groups for efficient catalysis and to reach the transition state. Adaptive substrate recognition is a well-known concept; however, it has been poorly characterized at a structural level because of its dynamic nature. Here, we provide a detailed mechanism for an induced-fit process at atomic resolution. We take advantage of a slow, tight binding inhibitor-enzyme system, actinonin-peptide deformylase. Crystal structures of the initial open state and final closed state were solved, as well as those of several intermediate mimics captured during the process. Ligand-induced reshaping of a hydrophobic pocket drives closure of the active site, which is finally "zipped up" by additional binding interactions. Together with biochemical analyses, these data allow a coherent reconstruction of the sequence of events leading from the encounter complex to the key-lock binding state of the enzyme. A "movie" that reconstructs this entire process can be further extrapolated to catalysis. Trapping conformational States along ligand-binding dynamics of Peptide deformylase: the impact of induced fit on enzyme catalysis.,Fieulaine S, Boularot A, Artaud I, Desmadril M, Dardel F, Meinnel T, Giglione C PLoS Biol. 2011 May;9(5):e1001066. Epub 2011 May 24. PMID:21629676 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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