Two Structures of the Catalytic Domain of Phosphorylase Kinase
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Two structures of the catalytic domain of phosphorylase kinase: an active protein kinase complexed with substrate analogue and product DJ Owen §, MEM Noble§, EF Garman, AC Papageorgiou t and LN Johnson* Laboratory of Molecular Biophysics and Oxford Centre for Molecular Sciences, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK Background: Control of intracellular events by protein Conclusions: The overall structure of Phkytrnc is similar phosphorylation is promoted by specific protein kinases. to that of the catalytic core of other protein kinases. It All the known protein kinases possess a common struc- consists of two domains joined on one edge by a 'hinge', ture that defines a catalytically competent entity termed with the catalytic site located in the cleft between the the 'kinase catalytic core'. Within this common structural domains. Phkytrnc is constitutively active, aid lacks the framework each kinase displays its own unique substrate need for an activatory phosphorylation event that is essen- specificity, and a regulatory mechanism that may be mod- tial for many kinases. The structure exhibits an essentially ulated by association with other proteins. Structural stud- 'closed' conformation of the domains which is similar to ies of phosphorylase kinase (Phk), the major substrate of that of cAPK complexed with substrates. The phosphory- which is glycogen phosphorylase, may be expected to lated residue that is located at the domain interface in shed light on its regulation. many protein kinases and that is believed to stabilize an Results: We report two crystal structures of the catalytic active conformation is substituted by a glutamate in core (residues 1-298; Phkytrnc) of the y-subunit of rabbit Phkytrnc. The glutamate, in a similar manner to the muscle phosphorylase kinase: the binary complex with phosphorylated residue in other protein kinases, interacts Mn2+/>3-y-imidoadenosine 5'-triphosphate (AMPPNP) with an arginine adjacent to the catalytic aspartate but to a resolution of 2.6 A and the binary complex with does not participate in interdomain contacts. The interac- Mg 2+/ADP to a resolution of 3.0 A. The structures were tions between the enzyme and the nucleotide product of solved by molecular replacement using the cAMP-depen- its activity, Mg2+/ADP, explain the inhibitory properties dent protein kinase (cAPK) as a model. of the nucleotides that are observed in kinetic studies. Structure 15 May 1995, 3:467-482 Key words: kinase, phosphorylase, phosphorylation, regulation, X-ray crystallography Introduction altered intracellular concentrations of Ca2 +. Signals that Protein modification by phosphorylation and dephos- regulate Phk activity originate from the interaction of phorylation, catalyzed by members of the protein kinase extracellular compounds with their tissue-specific cognate and protein phosphatase families, respectively, is a ubiqui- receptors. These compounds include the catecholamines tous regulatory mechanism in eukaryotic cells. It is a adrenaline and nor-adrenaline, and the peptide hormones readily reversible dynamic, switching mechanism that insulin, glucagon, angiotensin and vasopressin. Additional alters the biological function of a protein by modulating control of Phk activity comes from signals involved in the its structure and/or activity [1]. Glycogen phosphorylase energy balance of the cell and from neuronal signals that kinase (Phk) was discovered in 1955 and was the first stimulate the release of Ca2+ from intracellular stores protein kinase to be recognized and characterized [2,3]. [5,6]. It is this Ca2 + signal that also stimulates muscle For approximately 10 years after this observation, func- contraction. Consequently, the signal that initiates the tional control by reversible phosphorylation was thought energy-requiring process of muscle contraction also stim- to be a peculiarity of glycogen metabolism. Following ulates the breakdown of glycogen, the cell's major energy the discovery in 1968 of cAMP-dependent protein store. By transducing and integrating these signals, Phk is kinase (cAPK) [4], an enzyme with broader specificity able to coordinate the energy requirements and energy and the capability of phosphorylating a number of availability not only of individual cells but also of the diverse proteins, the importance of phosphorylation in entire organism. other regulatory mechanisms was recognized. The major physiological substrate of Phk is glycogen Phk is one of the largest and most complex of the known phosphorylase, although other substrates, such as glyco- protein kinases, and is central to the regulation of glyco- gen synthase, troponin I and the 3-subunit of Phk gen metabolism. This multimeric protein transduces and itself, have been identified in in vitro studies. Phk cat- integrates signals that affect glycogen metabolism; signals alyzes the activation of glycogen phosphorylase through take the form of multiple phosphorylation events and phosphorylation of a single residue, Serl4. *Corresponding author. §Joint first authors. t Present address: Department of Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK. © Current Biology Ltd ISSN 0969-2126 467 468 Structure 1995, Vol 3 No 5 Fig. 1. Schematic representation of the Phk y-subunit. The catalytic domain is coloured red and the calmodulin-bind- ing regulatory domain iscoloured blue. The Phk holoenzyme is hexadecameric, displaying the cleft between the two lobes, with the nucleotide sub- subunit stoichiometry (at3y) 4 with a total molecular strate interacting mainly with the small N-terminal weight of approximately 1.3 x 103 kDa. The a-, 3- and 3-sheet lobe, and peptide substrate mainly with the large B-subunits are regulatory whereas the y-subunit is cat- C-terminal at-helical lobe. A stretch of amino acids, alytic. The a- and 3-subunits (Mr 145000 and 128000, termed the activation loop, is situated at the domain respectively) transmit regulatory information via their interface at the 'mouth' of the cleft between the two phosphorylation state. Protein kinases known to phospho- domains, and comes into close proximity with the pep- rylate the a- and 3-subunits include cAPK, AMP-depen- tide substrate. This loop has been implicated in the dent protein kinase (APK), and Phk itself [7,8]. The Ca2+ off/on switching of many kinases by phosphorylation sensitivity of the holoenzyme is conferred by the 8-subunit and in the binding of regulatory subunits and peptide (Mr17000), which is essentially identical in sequence to substrate to the kinase domain. calmodulin [9]. The y-subunit (Mr45000; Fig. 1) contains a kinase catalytic domain [10], a motif delineated by the Here we report the structure, at 2.6 A resolution, of the analysis of primary sequences of many protein kinases, and kinase catalytic core of the Phk y-subunit (Phkytrnc; a calmodulin-binding domain [11]. The calmodulin-bind- residues 1-298) complexed with Mn2+/AMPPNP (a ing domain may act to regulate activity through a pseudo- non-hydrolyzable analogue of the nucleotide substrate substrate mechanism similar to that of myosin light chain Mg2+/ATP) and the structure of Phkytrnc complexed kinase (MLCK) whereby the Ca2+-bound form of with the nucleotide product of the phosphorylation calmodulin can compete for the binding of a pseudosub- reaction, Mg2+/ADP, at 3.0 A resolution. strate sequence contained elsewhere in the protein [12,13]. The Phk catalytic domain, residues 1-298 of the Phk -y-subunit, has been expressed in Escherichia coli and puri- Results fied [14-16]. It displays activity comparable to that of the The structure of Phkytrnc activated holoenzyme and, as expected, exhibits no regula- The crystal structure of Phkytrnc was solved initially at tion by Ca2 + or phosphorylation signals. 3.0 A resolution, by molecular replacement, using the structure of the catalytic core of cAPK (residues 43-280) Structural analyses of cAPK complexed with a variety of (protein databank [PDB] number 4CPK) as the search inhibitors, substrates and substrate analogues have defined object and data collected from crystals grown in the pres- the basic architecture of the kinase domain and the essen- ence of Mg2+/ATP. The structure was built with refer- tial features of substrate recognition [17-20]. The results ence to the O database [25] and had satisfactory of structural studies on three other serine/threonine stereochemistry (Table 1). Subsequently, data were col- kinases - the human cyclin-dependent kinase (CDK2) lected to 2.6 A resolution at 100 K from a crystal grown [21], mitogen-activated protein kinase (MAPK; also in the presence of Mn2+/AMPPNP. The model obtained known as ERK2) [22], and twitchin kinase [23] - and at 3.0 A resolution was refined against the higher resolu- on the first tyrosine kinase [24] have confirmed the struc- tion, low temperature data, and will be discussed in detail ture of the kinase fold and have begun to offer insights here (see Table 1). Inspection of the two structures into their regulatory mechanisms. The kinase catalytic revealed that the 3.0 A resolution structure was, in fact, core is bilobal in structure, with the two lobes joined by complexed with Mg2 +/ADP rather than Mg 2+/ATP. a single segment of polypeptide chain that appears to The structure of the Mg2+/ADP complex will be function as a 'pivot' about which the two lobes can rotate discussed only where it differs from that of the with respect to one another. The substrates bind in the Mn2 +/AMPPNP complex. Two structures of phosphorylase kinase Owen et al.