Motion in Adenylate Kinase (ADK) [adk]

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Classification Known Domain Motion, Hinge Mechanism [D-h-2]

Structures 1AK3 Conformation 1 1AKE Conformation 2 [ PartsList ] 1ANK Conformation 3 [ PartsList ] 3ADK Conformation 4 [ PartsList ]

Description 2 interdomain linkages and 4 hinges (one involves kinking helix). 60 degree rotation from 1st pair of hinges, 30 degree from 2nd pair, 90 degree total. In large variants of adenylate kinase the AMP and ATP substrates are buried by a domain rotating by 90 degrees. The mobile domain is linked to the rest of the protein by two helices packed together in an antiparallel fashion. During the closure, deformations take place in four localized regions, called joints, near the N and C termini of these helices. Three of these joints have simple motions that can be well approximated by rotations of three torsion angles, but the joint that makes contact with the ligand involves motion throughout an extended loop: i.e. two torsions on either side of a reverse turn change significantly. The main chain atoms of the joints have few packing constraints. The first pair of joints is responsible for approximately 30 degrees of the total rotation and the second pair for the remaining approximately 60 degrees. These movements carries along the regions between the joints, the two helices and the rest of the mobile domain, to a first approximation, as rigid bodies. ADK also has a shear motion when the first substrate, AMP, binds: i.e. in moving from the conformation of 3ADK to 1AK3, 3 helices with acrossed geometry shift 1-2 Angstroms to rearrange the geometry of the nucleotide binding site slightly.

Particular values describing motion Creation Date = 19970822 Experimental Methods = x (Traditional x-ray) Modification Date = 1999-11-04 14:04:40.000

References G E Schulz, C W Muller and K Diederichs (1990). Induced-fit movement in adenylate kinases. J. Mol. Biol. 213: 627-630. [Medline info for 9615437] K Diederichs and G E Schulz (1991). Refined structure of the complex between adenylate kinase from beef heart mitochondrial matrix and its substrate AMP at 1.85 angstrom resolution. J. Mol. Biol. 217: 541-549. [Medline info for 9615437] M B Berry, B Meador, T Bilderback, P Liang, M Glaser and J G N Phillips (1994). The closed conformation of a highly flexible protein: The structure of E. coli adenylate kinase with bound AMP and AMPPNP. Proteins: Struc. Func. Genet. 19: 183-198. [Medline info for 9615437] M Gerstein, G Schulz and C Chothia (1993). Domain Closure in Adenylate Kinase: Joints on Either Side of Two Helices Close Like Neighboring Fingers. J. Mol. Biol. 229: 494-501. [Medline info for 93156056]

Data and Graphics Graphic-2 Small shearing motion when the AMP binds (unrelated to major hinge motion). Graphic-3 The two hinges on either side of helix 7. Graphic-1 Overall motion. Adenylate Kinase -- the movie Courtesy of Clemens Vonrhein, Gerd J Schlauderer and Georg E Schulz.

GO terms associated with structures Molecular function nucleotide kinase activity, adenylate kinase activity, ATP binding Cellular component cytoplasm Biological process nucleobase, nucleoside, nucleotide and nucleic acid metabolism, ATP metabolism

Morphs

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Best representative Morph Morph name Structure #1 Structure #2 Residues [ ] [ ]

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Copyright 1995-2005 M. Gerstein, W. Krebs, S. Flores, N. Echols, and others
Email: Mark.Gerstein _at_ yale.edu