1Q97

The structure of the Saccharomyces cerevisiae SR protein kinase, Sky1p, with bound ATP

Summary for 1Q97

• Entry DOI: 10.2210/pdb1q97/pdb
• Related: 1q8y 1q8z 1q99
• Descriptor: SR protein kinase, MAGNESIUM ION, SULFATE ION, ... (7 entities in total)
• Functional Keywords: protein kinase, transferase
• Biological source: Saccharomyces cerevisiae (baker's yeast); More
• Total number of polymer chains: 2
• Total formula weight: 87123.98

Authors

Nolen, B.,Ngo, J.,Chakrabarti, S.,Vu, D.,Adams, J.A.,Ghosh, G. (deposition date: 2003-08-22, release date: 2003-09-23, Last modification date: 2024-02-14)

Primary citation

Nolen, B.,Ngo, J.,Chakrabarti, S.,Vu, D.,Adams, J.A.,Ghosh, G.
Nucleotide-Induced Conformational Changes in the Saccharomyces cerevisiae SR Protein Kinase, Sky1p, Revealed by X-ray Crystallography
Biochemistry, 42:9575-9585, 2003

PubMed Abstract: Conformational changes are thought to play a key role in the function of active protein kinases, although little is known about how these changes relate to the mechanism of phosphorylation. Here we present four high-resolution structures of a single crystal form of Sky1p, a constitutively active serine kinase implicated in yeast RNA processing, each in a different state of nucleotide binding. By comparing the apoenzyme structure to the ADP- and ATP-bound Sky1p structures, we have revealed conformational changes caused by ATP binding or conversion from nucleotide reactant to product. Rotation of the small lobe of the kinase closes the cleft upon binding, allowing the nucleotide to interact with residues from both lobes of the kinase, although some interactions thought to be important for phosphotransfer are missing in the ATP-containing structure. In the apoenzyme, a kinase-conserved phosphate-anchoring loop is in a twisted conformation that is incompatible with ADP and ATP binding, providing a potential mechanism for facilitating ADP release in Sky1p. The nonhydrolyzable ATP analogue AMP-PNP binds in a unique mode that fails to induce lobe closure. This observation, along with comparisons between the two independent molecules in the asymmetric unit of each structure, has provided new molecular details about how the nucleotide binds and induces closure. Finally, we have used mutational analysis to establish the importance of a glycine within the linker that connects the two lobes of Sky1p.

PubMed: 12911299
DOI: 10.1021/bi0344331

Experimental method

X-RAY DIFFRACTION (2.3 Å)