3mkn

Crystal structure of the E. coli pyrimidine nucleosidase YeiK bound to a competitive inhibitor

spinqualitylabelsall models 3mkn, resolution 2.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3mkn is a 4 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CA, DNB Related: 1q8f, 3b9x, 3mkm Gene: YeiK (Escherichia coli) Activity: Ribosylpyrimidine nucleosidase, with EC number 3.2.2.8 Resources: FirstGlance, OCA, RCSB, PDBsum Function [C3T3U2_ECOLX] Hydrolyzes cytidine or uridine to ribose and cytosine or uracil, respectively. Has a clear preference for cytidine over uridine. Strictly specific for ribonucleosides (By similarity).[HAMAP-Rule:MF_01433] Publication Abstract from PubMed Conformational changes modulate macromolecular function by promoting the specific binding of ligands (such as in antigen recognition) or the stabilization of transition states in enzymatic reactions. However, quantitative characterization of the energetics underlying dynamic structural interconversions is still challenging and lacks a unified method. Here, we introduce a novel in silico approach based on the combined use of essential dynamics sampling and nonequilibrium free-energy calculations to obtain quantitative data on conformational energy landscapes. This technique allows the unbiased investigation of highly complex rearrangements, and does not require the crucial definition of user-defined collective variables. We show that free-energy values derived from profiles connecting the unliganded and ligand-bound X-ray structures of a bacterial nucleoside hydrolase match the experimental binding constant. This approach also provides first evidence for a rate-limiting character of the conformational transition in this enzyme, and an unexpected role of the protonation state of a single residue in regulating substrate binding and product release. Energy Landscapes Associated with Macromolecular Conformational Changes from Endpoint Structures.,Fornili A, Giabbai B, Garau G, Degano M J Am Chem Soc. 2010 Nov 17. PMID:21082835 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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