Motion in cAMP-dependent Protein Kinase (catalytic domain) [pka]

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

Structures 1APM Another structure [ PartsList ] 1ATP With peptide inhibitorClosed Ternary complex [ PartsList ] 1CTP Open [ PartsList ] 1CMK [ PartsList ] 1CDK [ PartsList ]

Description 1st set of hinges, involving 3 interdomain linkages, produces 12 degree rotation of domain cores (with ~3 Angstrom shift). 2nd set of hinges produces further 6 degree rotation of a loop. 1 shearing interface between domains. Structures of 2 conformations have been solved but only 1 has been deposited in the Protein Data Bank. The catalytic subunit of cAMP-dependent protein kinase has an elaborate multi-part hinged motion, which involves at least five distinct hinges, split into the two sets. Containing two domains, one large and one small, the structure of the catalytic subunit has been solved in binary and ternary complexes with an inhibitory peptide and in an apo form. In comparing the apo and either complex form, the core of the small domain rotates ~12 degrees relative to that of the large one. The small domain is principally connected to the large domain through three roughly parallel peptide linkages, which deform as hinges upon closure. In addition, through the deformation of two more hinges a loop in the small domain near the binding pocket rotates a further 6 degrees down into the interdomain cleft. Partly because of the size of the interdomain cleft, which has to accommodate a 15 residue peptide, the protein kinase motion does not involve an extensive interdomain interface. There is, however, one helix in the small domain which moves in a shear fashion to maintain its contacts with the large domain throughout the motion.

Particular values describing motion Creation Date = 19970822 Modification Date = 19970822 Maximum Rotation (degrees) = 14 (total value) Maximum Translation (A) = 0.7 (total value) Experimental Methods = x (Traditional x-ray)

References R Karlsson, J H Zheng, N H Xuong, S S Taylor and J M Sowadski (1993). Structure of the mammalian catalytic subunit of cAMP-dependent protein kinase and an inhibitor peptide displays an open conformation. Acta Cryst D. 49: 381-388. [Medline info for 89125622] Zheng J; Knighton DR; Xuong NH; Taylor SS; Sowadski JM; Ten Eyck LF. Crystal structures of the myristylated catalytic subunit of cAMP-dependent protein kinase reveal open and closed conformations. Protein Science, 1993 Oct, 2(10):1559-73. [Medline info for 94073072]

Data and Graphics Graphic-2 Same as the first graphic but from a different direction. Graphic-3 Closeup of small domain. Graphic-1 Overall motion can be broken into two motions (red lines and dotted red line).

GO terms associated with structures Molecular function ATP binding, cAMP-dependent protein kinase inhibitor activity, protein kinase activity, protein serine/threonine kinase activity Biological process protein amino acid phosphorylation, negative regulation of protein kinase activity

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