2rgx | pdb_00002rgx

Crystal Structure of Adenylate Kinase from Aquifex Aeolicus in complex with Ap5A

spinqualitylabelsall models 2rgx, resolution 1.90Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2rgx is a 1 chain structure with sequence from "aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: AP5, ZN Related: 2rh5 Gene: adk ("Aquifex aeolicus" Huber and Stetter 2001) Activity: Adenylate kinase, with EC number 2.7.4.3 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [KAD_AQUAE] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth (By similarity). 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 mechanisms by which enzymes achieve extraordinary rate acceleration and specificity have long been of key interest in biochemistry. It is generally recognized that substrate binding coupled to conformational changes of the substrate-enzyme complex aligns the reactive groups in an optimal environment for efficient chemistry. Although chemical mechanisms have been elucidated for many enzymes, the question of how enzymes achieve the catalytically competent state has only recently become approachable by experiment and computation. Here we show crystallographic evidence for conformational substates along the trajectory towards the catalytically competent 'closed' state in the ligand-free form of the enzyme adenylate kinase. Molecular dynamics simulations indicate that these partially closed conformations are sampled in nanoseconds, whereas nuclear magnetic resonance and single-molecule fluorescence resonance energy transfer reveal rare sampling of a fully closed conformation occurring on the microsecond-to-millisecond timescale. Thus, the larger-scale motions in substrate-free adenylate kinase are not random, but preferentially follow the pathways that create the configuration capable of proficient chemistry. Such preferred directionality, encoded in the fold, may contribute to catalysis in many enzymes. Intrinsic motions along an enzymatic reaction trajectory.,Henzler-Wildman KA, Thai V, Lei M, Ott M, Wolf-Watz M, Fenn T, Pozharski E, Wilson MA, Petsko GA, Karplus M, Hubner CG, Kern D Nature. 2007 Dec 6;450(7171):838-44. Epub 2007 Nov 18. PMID:18026086 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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