1NE6

Crystal structure of Sp-cAMP binding R1a subunit of cAMP-dependent protein kinase

Summary for 1NE6

• Entry DOI: 10.2210/pdb1ne6/pdb
• Related: 1CX4 1NE4 1RGS
• Descriptor: cAMP-dependent protein kinase type I-alpha regulatory chain, 6-(6-AMINO-PURIN-9-YL)-2-THIOXO-TETRAHYDRO-2-FURO[3,2-D][1,3,2]DIOXAPHOSPHININE-2,7-DIOL (3 entities in total)
• Functional Keywords: camp-dependent protein kinase, r1a subunit, camp analog, sp-camp, hydrolase
• Biological source: Bos taurus (cattle)
• Total number of polymer chains: 1
• Total formula weight: 32570.65

Authors

Wu, J.,Jones, J.M.,Xuong, N.H.,Taylor, S.S. (deposition date: 2002-12-10, release date: 2004-01-13, Last modification date: 2023-08-16)

Primary citation

Wu, J.,Jones, J.M.,Xuong, N.H.,Eyck, L.F.,Taylor, S.S.
Crystal Structures of RIalpha Subunit of Cyclic Adenosine 5'-Monophosphate (cAMP)-Dependent Protein Kinase Complexed with (R(p))-Adenosine 3',5'-Cyclic Monophosphothioate and (S(p))-Adenosine 3',5'-Cyclic Monophosphothioate, the Phosphothioate Analogues of cAMP.
Biochemistry, 43:6620-6629, 2004

PubMed Abstract: Cyclic adenosine 5'-monophosphate (cAMP) is an ancient signaling molecule, and in vertebrates, a primary target for cAMP is cAMP-dependent protein kinase (PKA). (R(p))-adenosine 3',5'-cyclic monophosphothioate ((R(p))-cAMPS) and its analogues are the only known competitive inhibitors and antagonists for cAMP activation of PKA, while (S(p))-adenosine 3',5'-cyclic monophosphothioate ((S(p))-cAMPS) functions as an agonist. The crystal structures of a Delta(1-91) deletion mutant of the RIalpha regulatory subunit of PKA bound to (R(p))-cAMPS and (S(p))-cAMPS were determined at 2.4 and 2.3 A resolution, respectively. While the structures are similar to each other and to the crystal structure of RIalpha bound to cAMP, differences in the dynamical properties of the protein when (R(p))-cAMPS is bound are apparent. The structures highlight the critical importance of the exocyclic oxygen's interaction with the invariant arginine in the phosphate binding cassette (PBC) and the importance of this interaction for the dynamical properties of the interactions that radiate out from the PBC. The conformations of the phosphate binding cassettes containing two invariant arginine residues (Arg209 on domain A, and Arg333 on domain B) are somewhat different due to the sulfur interacting with this arginine. Furthermore, the B-site ligand together with the entire domain B show significant differences in their overall dynamic properties in the crystal structure of Delta(1-91) RIalpha complexed with (R(p))-cAMPS phosphothioate analogue ((R(p))-RIalpha) compared to the cAMP- and (S(p))-cAMPS-bound type I and II regulatory subunits, based on the temperature factors. In all structures, two structural solvent molecules exist within the A-site ligand binding pocket; both mediate water-bridged interactions between the ligand and the protein. No structured waters are in the B-site pocket. Owing to the higher resolution data, the N-terminal segment (109-117) of the RIalpha subunit can also be traced. This strand forms an intermolecular antiparallel beta-sheet with the same strand in an adjacent molecule and implies that the RIalpha subunit can form a weak homodimer even in the absence of its dimerization domain.

PubMed: 15157095
DOI: 10.1021/bi0302503

Experimental method

X-RAY DIFFRACTION (2.3 Å)