3MKM

Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK (Apo-form)

Summary for 3MKM

• Entry DOI: 10.2210/pdb3mkm/pdb
• Related: 1Q8F 3B9X 3MKN
• Descriptor: Putative uncharacterized protein YeiK, CALCIUM ION (3 entities in total)
• Functional Keywords: pyrimidine nucleoside hydrolase, bacterial nucleosidase, nucleotide metabolism, metalloenzyme, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 136336.81

Authors

Garau, G.,Fornili, A.,Giabbai, B.,Degano, M. (deposition date: 2010-04-15, release date: 2010-12-01, Last modification date: 2023-11-01)

Primary citation

Fornili, A.,Giabbai, B.,Garau, G.,Degano, M.
Energy Landscapes Associated with Macromolecular Conformational Changes from Endpoint Structures
J.Am.Chem.Soc., 132:17570-17577, 2010

PubMed Abstract: 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.

PubMed: 21082835
DOI: 10.1021/ja107640u

Experimental method

X-RAY DIFFRACTION (2.2 Å)