sign in sign up
<<
Home , Creatine kinase, UMP kinase

View metadata, citation and similar papers at core.ac.uk brought to you by CORE

provided by Elsevier - Publisher Connector

Minireview 413

How do transfer phosphoryl groups? Allan Matte†, Leslie W Tari and Louis TJ Delbaere*

Understanding how phosphoryl transfer is accomplished by binding, various modes of nucleotide binding, kinases, a ubiquitous group of , is central to many substrate orientation and geometry, active-site organi- biochemical processes. Qualitative analysis of the crystal zation, metal-ion coordination and electrostatic effects structures of –substrate complexes of kinases (Figure 1). Here, we present an overview of some struc- reveals structural features of these enzymes important to tural features which relate to the activity of these enzymes. phosphoryl transfer. Recently determined crystal structures Other reviews on phosphoryl transfer have been pub- which mimic the transition state complex have added new lished previously [1–5]. insight into the debate as to whether kinases use associative or dissociative mechanisms of . Conformational changes upon substrate binding Comparison of the crystallographic structures of many Address: Department of Biochemistry, University of Saskatchewan, nucleotide-dependent phosphoryl transfer enzymes in the Saskatoon, Saskatchewan S7N 5E5, Canada. presence and absence of substrates or substrate analogs †Present address: Biotechnology Research Institute, 6100 reveals both global and local changes in protein structure. Royalmount Avenue, Montreal QC H4P 2R2, Canada. This process can be viewed in one of two ways. Either binding of one or more substrates induces a change in con- *Corresponding author. formation or, alternatively, binding of one or more sub- E-mail: [email protected] strates serves to trap the protein in a particular conforma- Structure 15 April 1998, 6:413–419 tional state which otherwise already exists in solution. In http://biomednet.com/elecref/0969212600600413 this latter view, substrate binding simply shifts the equi- © Current Biology Ltd ISSN 0969-2126 librium distribution of structures to one conformational state over another. Evidence from time-resolved fluores- cence studies on adenylate is in agreement with Kinases are a ubiquitous group of enzymes central to the latter of these two models [6]. many biochemical processes. The X-ray crystal structures of kinase–substrate complexes have revealed structural Global changes in structure usually involve hinge- features of these enzymes important to phosphoryl trans- bending motions [7–9] or rotation [10] of two or more fer, and have added new insight into the debate as to domains towards one another, resulting in the closure of whether kinases use associative or dissociative mecha- the active-site cleft (reviewed in [11,12]). In adenylate nisms of catalysis. kinases [13] and [8] there are synergistic effects on global conformational changes, with The transfer of the terminal phosphoryl group from one each substrate inducing a change in structure. These nucleotide to another, or to a (by enzymes structural changes act to position enzyme sidechains which we will term ‘small molecule kinases’), or to a appropriately around the substrates and to sequester the protein substrate (by protein kinases) is a fundamental substrates so as to prevent the wasteful hydrolysis of process in many aspects of , gene regulation nucleotides or other phosphoryl-containing substrates and signal transduction. With a wealth of experimental prior to catalysis. In other enzymes, such as phospho- data, obtained using many biochemical and structural enolpyruvate carboxykinase, large domain movements are techniques, this should be among the best understood of observed upon ATP binding, although evidence for syn- enzyme-catalyzed reactions. In view of the enormous ergistic structural effects based on X-ray crystallography variety of proteins which carry out these reactions, two is so far lacking [7]. A unique, swiveling-domain mecha- important questions need to be addressed. What structural nism, involving apparently two conformational states, has features of these enzymes and their interactions with sub- been proposed for phosphoryl transfer in pyruvate phos- strates are potentially important to the process of phos- phate dikinase based on the crystal structure of the native phoryl transfer? and how do these features relate to the enzyme [14]. Nucleoside diphosphate kinase, an enzyme mechanisms and transition states of catalysis? with four or six subunits depending on the source, is unusual in that it does not show large-scale changes in This review focuses primarily on the crystal structures of structure upon substrate binding [15–17]. enzyme–substrate complexes of kinases and, in particular, what these structures tell us about the process of phos- In addition to the global changes in structure accompany- phoryl transfer. Many structural parameters may poten- ing nucleotide binding, local changes in protein structure, tially contribute to the process of phosphoryl transfer, as well as alterations to the nucleotide conformation com- including global and local conformational changes upon pared to its structure in free solution, may occur. Smaller 414 Structure 1998, Vol 6 No 4

Figure 1

Structural parameters influencing phosphoryl transfer by kinases. Nucleotides may be bound with the β- and γ-phosphoryl groups in an Positively charged Second divalent 2+

eclipsed conformation, resulting in a sterically residue(s) cation (Mn ) and energetically strained substrate ready for α-helix H

2+ dipole catalysis. Mg binding may help to promote O – H this structure, as well as positioning the γ- phosphoryl group with respect to the second substrate so as to create the correct geometry + O for phosphoryl transfer. Nucleotide-binding H H –OOC motifs (e.g. P loop or -rich loop) also + serve to orient the nucleotide in the correct – position for phosphoryl transfer. Positively O–C charged residues, including the conserved of the P-loop motif or the positive CH terminus of an α-helix dipole, may assist in 2 stabilizing the phosphoryl group during transfer. P loop, glycine-rich loop or other motif H O In the case of an associative mechanism, Mg2+ O H Geometrical alignment H for 'in-line' transfer would also contribute by increasing the H Purine- or electrophilicity of the γ-phosphorous atom by pyrimidine-binding pocket withdrawing charge via its interactions with the oxygen atoms. In some enzymes, such as Nucleotide-associated 2+ phosphoenolpyruvate carboxykinase, a second metal (Mg ) metal ion may further increase the electrophilicity Structure of the transferred phosphoryl group, impart additional orientation effects on the substrates, them to the protein, while at the same time through both local and global (domain–domain) and play a role in forming the transition state. permitting changes in metal environment during motions. It should be noted that any single Water molecules which complete the catalysis. Usually, positively charged sidechains enzyme would not be expected to show all of coordination sphere of the metal(s) help anchor bind and position substrates for catalysis the possible features depicted.

changes in structure are seen in Escherichia coli phospho- an unusual case with UMP/CMP kinase, only water [20]. , where binding of ADP–Mg2+ and fructose- In phosphoenolpyruvate carboxykinase, Mg2+ coordina- 1,6-bisphosphate induce a shear motion within a single tion orients the β- and γ-phosphoryl groups in a high- domain [18]. In phosphoenolpyruvate carboxykinase, energy, eclipsed conformation resulting in increased significant changes in the adenine-binding region are electrostatic repulsion between the phosphoryl groups observed upon complexation with Mg2+–ATP [7]. Crys- which may activate ATP for catalysis [7,21]. Presumably tallographic analysis of several complexes of cAMP- Mg2+ also assists in orienting the γ-phosphoryl group ‘in- dependent [12,19] has demonstrated local line’ with respect to the second substrate, creating the flexibility in the glycine-rich loop, a conserved element correct geometry to complete phosphoryl transfer. responsible for interacting with ATP in the protein kinase catalytic core. In ADP- or GDP-bound structures, in which a second phosphorylated is present, the coordination of the Role of divalent cations Mg2+ changes so that in many instances it acts to bridge Essentially all kinases require a Mg2+–nucleotide complex the β-phosphoryl group of the ADP and the phosphoryl as one of the enzyme substrates, an exception being the group of the second product. This mode of Mg2+ binding first partial reaction catalyzed by nucleoside diphosphate is observed in the complexes of Trypanosoma brucei phos- kinase, which can proceed independently of Mg2+ [15]. phoglycerate kinase with 3-phosphoglycerate and ADP The orientation of the Mg2+ ion relative to the substrates [8], with fructose 1,6-bisphosphate seems to fall into one of two patterns. and ADP [18], and with glycerol phosphate and ADP [22]. With bound ATP or GTP, the Mg2+ is usually coordinated to the β- and γ-phosphoryl groups, but may also be coordi- At least two kinases, [23] and phospho- nated to the α-, β- and γ-phosphates [9]. High-resolution enolpyruvate carboxykinase [24], require two divalent structures have shown that between two and four water cations for full activity. Pyruvate kinase has an additional molecules make up part of the Mg2+ coordination sphere. requirement for a monovalent cation. For both enzymes, The ligands completing the octahedral coordination may Mg2+ is a cosubstrate with the nucleotide, while the be oxygen atoms from the sidechains of , , second cation, a transition metal, has a separate distinct or residues of the protein or, in . Electron paramagnetic resonance (EPR) Minireview Enzyme-catalyzed phosphoryl transfer Matte, Tari and Delbaere 415

Figure 2

Structural organization of the bimetal cluster in phosphoenolpyruvate carboxykinase. Detailed stereo view of substrate/metal binding in the . Mg2+ is shown in blue, Mn2+ in green and water molecules are in red. Potential hydrogen bonds and/or electrostatic interactions are shown as yellow dotted lines. Both metals possess octahedral coordination spheres which are partially completed by water molecules. Mg2+ and a lysine residue neutralize electrostatic repulsions between phosphate oxygen atoms on ATP, promoting the formation of a high-energy conformer which eclipses the oxygens of the β- and γ- phosphates and orients the triphosphate chain so that it is aligned towards pyruvate. Mn2+ and an bridge ATP and pyruvate, neutralizing electrostatic repulsions between the anionic substrates, facilitating proper substrate alignment and activating both substrates through direct and water- mediated interactions. One arginine electrostatically promotes and stabilizes second arginine stabilizes enolate formation pyruvate. Mn2+ acts in concert with both pyruvate enolate formation via direct ionic through neutralization of the negative charge to promote and stabilize enolate interactions with the enolate oxygen, while a on the adjacent carboxylate group on formation. spectroscopy of various substrate and inhibitor complexes is the phosphate-binding (P-loop) motif [32,33]. In this of pyruvate kinase indicates that Mn2+ coordinates to both motif, conserved glycine residues make mainchain con- ATP and oxalate, a structural analog of the enolate of tacts with phosphoryl groups, while the oxygen atom of a pyruvate, the proposed reaction intermediate [25,26]. Two conserved serine or threonine residue makes up one divalent cations are observed at the active site of cAMP- ligand of the Mg2+ ion. A conserved lysine residue dependent protein kinase, although only the Mg2+ ion usually coordinates to the β- and γ-phosphoryl groups, bound to the β- and γ-phosphoryl groups appears to acti- and plays a crucial role in phosphoryl transfer. It is not vate catalysis [27,28]. clear whether this lysine, or other basic residue, ‘follows’ the transferred phosphoryl moiety during catalysis, Recently, the crystal structure of phosphoenolpyruvate [9,27,32] or rather forms part of a structural template for carboxykinase with both Mg2+ and Mn2+, as well as pyru- the reaction [34]. Protein kinase catalytic cores also vate and ATP, has been solved [21]. This structure pro- contain a glycine-rich motif responsible for interacting vides insight into how both metals participate in the with ATP which is both different in sequence and struc- process of synergistic activation of the enzyme (Figure 2). ture compared to the P loop [35]. In some kinases, the The Mg2+ cation has identical geometry to that found in positive terminus of an α-helix dipole points towards the phosphoenolpyruvate carboxykinase complexed with ATP– β-orγ-phosphate, thereby imparting a stabilizing effect Mg2+–oxalate [7]. Mn2+ bridges the γ-phosphoryl group of during phosphoryl transfer [8,9,18]. ATP and pyruvate via two water molecules. In the pro- posed transition state, Mn2+ displaces the waters to form There are less definitive sequence or structural patterns an inner-sphere complex with the enolate anion. Both relating to ribose and purine or pyrimidine binding. In metals appear specific for their respective binding sites, some kinases hydrophobic interactions sandwich the which can be explained by their relative Lewis acidity and adenine ring; these interactions may be combined with ionic radii. A similar mode of binding of the two metals one or more mainchain, or occasionally sidechain, hydro- was proposed previously using EPR and proton longitudi- gen bonds to N1, N6 or N7 of adenine. In other proteins, nal relaxation rate measurements [29–31]. such as nucleoside diphosphate kinase [15–17], phospho- fructokinase [18], and kinase [36], no specific Binding and orientation of nucleotide substrates polar contacts between the base and protein have been It is well known that kinases may bind their nucleotide observed. In fact, it appears that mainchain contacts with substrates, usually GTP or ATP, in a variety of ways the bases and the presence of a structural motif indepen- (reviewed in [32]). One structural motif commonly dent of sequence may be more important for adenine employed in a variety of ATP- and GTP-binding proteins binding, for example, as described for protein kinases and 416 Structure 1998, Vol 6 No 4

D-Ala:D-Ala adenine-binding sites, as well as pro- Do phosphoryl transfer reactions operate via an teins with the ATP grasp fold [37,38]. These observations associative or dissociative transition state? help to explain why no definitive sequence pattern for There has been considerable debate within the literature adenine binding has emerged, despite the large number of as to whether enzyme-catalyzed phosphoryl transfer reac- sequences which have been analyzed [39]. Another possi- tions operate primarily with an associative (SN2-like) or bility is a role for structural water molecules in mediating dissociative (SN1-like) transition state. A summary of the protein–base recognition [20]. two possible enzymatic mechanisms and the associated transition states for phosphoryl transfer is presented in Figure 3. Experimental studies on phosphoryl transfer by (a) Double displacement (ping-pong) mechanism small molecules ([40,41] and references cited therein) and model studies on the G protein p21Haras [42] have led to arguments in favor of a dissociative mechanism of catal- ysis in kinases and phosphatases. Others have made elegant arguments in favor of these enzymes operating with more of an associative character [2,3]. Various bio- chemical approaches have been used to tackle this ques- tion with enzymes in solution, yielding different results depending on the particular protein. Positional isotope exchange experiments on pyruvate kinase indicate that an associative transition state is operational [43], while kinetic studies on nucleoside diphosphate kinase [44] and secondary 18O isotope experiments with [45] in both cases suggest a dissociative transition state.

What structural evidence exists from crystal structures of enzyme–substrate complexes of kinases in favor of asso- ciative versus dissociative transition states? Many of the arguments in favor of associative [7,8,21,46–48] or disso- ciative [20] transition states for phosphoryl transfer have been based on the geometry and reaction coordinate dis- tances between the terminal phosphoryl group and its

Figure 3

Mechanisms and transition states for phosphoryl transfer reactions. Two catalytic mechanisms of phosphoryl transfer are commonly (b) encountered, either single (direct) displacement or double displacement (ping-pong) mechanisms. In the single displacement Associative transition state mechanism, all substrates must be bound to the enzyme, forming a Nucleotide Enolate anion ternary complex, before phosphoryl transfer can take place. With the double displacement mechanism, illustrated in (a), the nucleotide initially binds and donates a phosphoryl group to the enzyme, usually at O O OO OOC a histidinyl residue, generating a phospho–enzyme intermediate. The Adenosine O P O P O P OC enzyme-bound phosphoryl group is in turn donated to a second

O O O CH2 substrate yielding the final product. Nucleotides are depicted in yellow, the acceptor substrate in purple, and the transferred phosphoryl group Pentacoordinate (b) transition state in red. For either mechanism described above, the transition state for phosphoryl transfer may be described as one of two possibilities, either associative (SN2-like) or dissociative (SN1-like). In the Dissociative transition state associative case, the transition state is dominated by bond formation, and involves a pentagonal bipyrimidal (phosphorane) structure with the O O OO OOC axial ligands being the nucleophile of the attacking substrate and bridging oxygen atom between the β- and γ-phosphates, respectively. Adenosine O P O P P O O C The dissociative case involves a planar, trigonal, metaphosphate O – O O CH2 (PO3 ) structure, and is dominated by bond breaking. The two transition states are further defined by differences in charge Trigonal planar distribution, with a net charge of –3 on the phosphoryl group in the transition state associative case, and –1 on metaphosphate in the dissociative case. (metaphosphate) Various experimental criteria used to distinguish the two transition states have been reviewed elsewhere [3,41]. Structure Minireview Enzyme-catalyzed phosphoryl transfer Matte, Tari and Delbaere 417

Figure 4

Recent crystal structures of transition state analogs. (a) Stereo view of the active-site region of nucleoside diphosphate kinase 2+ complexed with ADP–Mg and AlF3, showing the transition state geometry [50]. The Al atom (magenta) is 2.5 Å from O7 of ADP and Nδ1 of His122, the site of phosphorylation. The Mg2+ ion (light blue sphere) is octahedrally coordinated by one F atom (green), oxygens of the α- and β-phosphates, and three water molecules (red spheres). A hydrogen bond is present (2.6 Å) between the 3′OH of the ribose and the bridging oxygen O7. Residues Lys16, Tyr56, Arg92 and Gly123 make interactions with the F atoms of AlF3. (b) Stereo view of the active- site region of UMP/CMP kinase with bound 2+ ADP–Mg , CMP and AlF3 [34]. Atoms are coloured as in (a). The distances between the Al atom and the oxygen atoms of ADP and CMP are 2.0 Å and 2.2 Å, respectively. The coordination sphere of the Mg2+ ion (light terminal phosphate of ADP, one F atom, and Lys19, Arg42, Arg93, Arg131 and Arg137 blue) consists of one oxygen atom from the four water molecules. The sidechains of interact with substrates at the active site.

acceptor substrate in ground state enzyme–substrate or atom is 2.0 Å from the bridging O of ADP and 2.2 Å from enzyme–inhibitor complexes. For the transition state to CMP, suggesting a significant amount of bond formation have some degree of associative character, these distances in the transition state. This study may represent the best are expected to be less than the sum of a P–O van der structural evidence so far in favor of an associative mecha- Waals contact and a P–O single bond (i.e. in the order of nism of phosphoryl transfer. In contrast, a similar study approximately 4.9 Å); in the dissociative case these dis- performed on nucleoside diphosphate kinase complexes 2+ – tances would be expected to be longer than this [3,47]. In with ADP–Mg and either BeF3 or AlF3 suggested cAMP-dependent protein kinase, an in-line, nucleophillic partial associative and dissociative character in the transi- attack with a pentacoordinate transition state has been tion state [50]. Finally, the crystal structure of human H- postulated [19,28]. In all cases, such analyses are beset by Ras bound to the GTPase-activating protein p120GAP 2+ the limitation that they represent, that is, the structural (GAP-334) with ADP, Mg and AlF3 has been recently arrangement prior to the actual phosphoryl transfer event. solved [51]. In this structure, the observed distances between the β-phosphoryl group of GDP and the catalytic In order to more rigorously distinguish between associa- water molecule (2.2 Å), the disposition of the Mg2+ ion tive and dissociative transition states in a structural way, it bridging the β-phosphoryl group of ADP and one of the F is necessary to have a view of the transition state complex. atoms of AlF3, and the orientation of additional positively There are obvious experimental challenges to identifying charged residues about the AlF3 group, which indicate the transition state for an enzyme-catalyzed phosphoryl charge neutralization of the transferred phosphoryl transfer process, whose lifetime is of the order 10–13 s, moiety, are together consistent with an associative transi- using structural techniques. However, the use of structural tion state. Interestingly, binding of the GTPase activator analogs of the γ-phosphoryl group transferred in these GAP-334 introduces a single arginine sidechain into the – reactions, such as tetrahedral BeF3 or trigonal planar AlF3 active-site region, bridging the GDP and AlF3 molecules (described in [49]), in complex with other substrates, in the complex. This result supports the importance of together permit snapshots of the ground state-like and charge neutralization during GTP hydrolysis and is also transition state-like structures, respectively. consistent with an associative-type mechanism.

Recently, crystal structures of three enzymes in complex In the course of the phosphoryl transfer reaction with a dis- with these analogs have been determined (Figure 4). sociative-type transition state, the largest change in charge Crystal structures of UMP/CMP kinase with substrates is expected to be for the bridging oxygen atom which con- β γ and either BeF2 or AlF3 indicate that charged arginine nects the - and -phosphoryl groups [42]. The observation residues rearrange during catalysis to stabilize negative of a hydrogen bond between the protein backbone and charges on the transferred phosphoryl group, in support of bridging O in p21Haras has been interpreted as evidence an associative mechanism [34]. In this structure, the Al for a dissociative transition state through stabilization of 418 Structure 1998, Vol 6 No 4

the GDP leaving group [42]. Such hydrogen bonds are also 12. Cox, S., Radzio-Andzelm, E. & Taylor, S.S. (1994). Domain movements observed in the BeF – and AlF complexes of nucleoside in protein kinases. Curr. Opin. Struct. Biol. 4, 893–901. 3 3 13. Vonrhein, C., Schlauderer, G.J. & Schulz, G.E. (1995). Movie of the diphosphate kinase, although in this case the hydrogen structural changes during a catalytic cycle of nucleoside bond is donated by the substrate itself [50]. Such an inter- monophosphate kinases. Structure 3, 483–490. 14. Herzberg, O., et al., & Dunaway-Mariano, D. (1996). Swiveling-domain action is not inconsistent with an associative process; it is mechanism for enzymatic phosphotransfer between remote reaction also possible that such a hydrogen bond serves to stabilize sites. Proc. Natl. Acad. Sci. USA 93, 2652–2657. the orientation of the nucleotide during catalysis. 15. Williams, R.L., Oren, D.A., Muñoz-Dorado, J., Inouye, S., Inouye, M. & Arnold, E. (1993). Crystal structure of Myxococcus xanthus nucleoside diphosphate kinase and its interaction with a nucleotide Summary substrate at 2.0 Å resolution. J. Mol. Biol. 234, 1230–1247. 16. Moréra, S., et al., & Janin, J. (1994). Adenosine 5′-diphosphate There are a number of recurrent structural features of binding and the active site of nucleoside diphosphate kinase. kinases complexed with substrates or substrate analogs Biochemistry 33, 459–467. which contribute to phosphoryl transfer. These features 17. Cherfils, J., Moréra, S., Lascu, I., Véron, M. & Janin, J. (1994). X-ray structure of nucleoside diphosphate kinase complexed with thymidine include global and local conformational changes, the use diphosphate and Mg2+ at 2-Å resolution. Biochemistry 33, of Mg2+ and in some cases other divalent cations which 9062–9069. interact with the transferred phosphoryl group, and the 18. Shirakihara, Y. & Evans, P.R. (1988). Crystal structure of the complex of phosphofructokinase from Escherichia coli with its reaction use of positively charged residues to stabilize the putative products. J. Mol. Biol. 204, 973–994. transition state, to name but a few. We are left to wonder 19. Madhusudan, et al., & Sowadski, J.M. (1994). cAMP-dependent protein kinase: crystallographic insights into substrate recognition and whether the transition state for phosphoryl transfer from phosphotransfer. Protein Sci. 3, 176–187. nucleotides under catalytic versus non-catalytic condi- 20. Scheffzek, K., Kliche, W., Wiesmüller, L. & Reinstein, J. (1996). Crystal tions are genuinely different, or whether some enzymes structure of the complex of UMP/CMP kinase from Dictyostelium discoideum and the bisubstrate inhibitor P1-(5′-adenosyl) simply favor an associative over dissociative transition 5 ′ 2+ P -(5 -uridyl)pentaphosphate (UP5A) and Mg at 2.2 Å: implications state. Further application of linear free-energy relation- for water-mediated specificity. Biochemistry 35, 9716–9727. 2+ 2+ ships (LFERs) to kinases, as described for alkaline phos- 21. Tari, L.W., Matte, A., Goldie, H. & Delbaere, L.T.J. (1997). Mg –Mn clusters in enzyme-catalyzed phosphoryl-transfer reactions. Nat. phatase [52], should help to clarify this point. The Struct. Biol. 4, 990–994. continued development of novel experimental and theo- 22. Hurley, J.H., et al., & Remington, S.J. (1993). Structure of the regulatory complex of Escherichia coli IIIGlc with glycerol kinase. retical approaches to a variety of kinases will be necessary Science 259, 673–677. to help answer these questions. 23. Baek, Y.H. & Nowak, T. (1982). Kinetic evidence for a dual cation role for muscle pyruvate kinase. Arch. Biochem. Biophys. 217, 491–497. 24. Lee, M.H., Hebda, C.A. & Nowak, T. (1981). The role of cations in Acknowledgements avian liver phosphoenolpyruvate carboxykinase catalysis. J. Biol. We thank Wim Hol, Jacqueline Cherfils and Ilme Schlichting for providing Chem. 256, 12793–12801. coordinates prior to release. LWT is the recipient of a Medical Research 25. Buchbinder, J.L. & Reed, G.H. (1990). Electron paramagnetic Council Post-doctoral Fellowship from the Medical Research Council of resonance studies of the coordination schemes and site selectivities Canada. This work was supported by an operating grant from the Medical for divalent metal ions in complexes with pyruvate kinase. Research Council of Canada (LTJD). Biochemistry 29, 1799–1806. 26. Buchbinder, J.L., Baraniak, J., Frey, P.A. & Reed, G.H. (1993). References Stereochemistry of metal ion coordination to the terminal 1. Knowles, J.R. (1980). Enzyme-catalyzed phosphoryl transfer reactions. thiophosphoryl group of adenosine 5′-O-(3-thiotriphosphate) at the Annu. Rev. Biochem. 49, 877–919. active site of pyruvate kinase. Biochemistry 32, 14111–14116. 2. Knowles, J.R. (1982). Phosphotransfer enzymes: lessons from 27. Bossemeyer, D., Engh, R.A., Kinzel, V., Ponstingl, H. & Huber, R. stereochemistry. Fed. Proc. 41, 2424–2431. (1993). and substrate binding mechanism of the 3. Mildvan, A.S. & Fry, D.C. (1987). NMR studies of the mechanism of cAMP-dependent protein kinase catalytic subunit from porcine heart enzyme action. Adv. Enzymol. 59, 241–313. as deduced from the 2.0 Å structure of the complex with adenylyl 4. Frey, P.A. (1992). and : imidodiphosphate and inhibitor peptide PKI(5–24). EMBO J. 12, stereochemistry and covalent intermediates. In The Enzymes. 849–859. (Sigman, D.S., ed.) 20, pp. 141–186, Academic Press, New York. 28. Zheng, J., et al., & Sowadski, J.M. (1993). Crystal structure of the 5. Cleland, W.W. & Hengge, A.C. (1995). Mechanisms of phosphoryl catalytic subunit of cAMP-dependent protein kinase complexed with and acyl transfer. FASEB J. 9, 1585–1594. MgATP and peptide inhibitor. Biochemistry 32, 2154–2161. 6. Sinev, M.A., Sineva, E.V., Ittah, V. & Haas, E. (1996). Domain closure 29. Duffy, T.H. & Nowak, T. (1985). 1H and 31P relaxation rate studies of in . Biochemistry 35, 6425–6437. the interaction of phosphoenolpyruvate and its analogues with avian 7. Tari, L.W., Matte, A., Pugazhenthi, U., Goldie, H. & Delbaere, L.T.J. liver phosphoenolpyruvate carboxykinase. Biochemistry 24, (1996). Snapshot of an enzyme reaction intermediate in the structure 1152–1160. of the ATP–Mg2+–oxalate ternary complex of phosphoenolpyruvate 30. Hebda, C.A. & Nowak, T. (1982). Phosphoenolpyruvate carboxykinase. carboxykinase. Nat. Struct. Biol. 3, 355–363. Mn2+ and Mn2+ substrate complexes. J. Biol. Chem. 257, 5515–5522. 8. Bernstein, B.E., Michels, P.A.M. & Hol, W.G.J. (1997). Synergistic 31. Lee, M.H. & Nowak, T. (1984). -31 nuclear relaxation rate effects of substrate-induced conformational changes in studies of the nucleotides on phosphoenolpyruvate carboxykinase. phosphoglycerate kinase activation. Nature 385, 275–278. Biochemistry 23, 6506–6513. 9. Auerbach, G., et al., & Jacob, U. (1997). Closed structure of 32. Schulz, G.E. (1992). Binding of nucleotides by proteins. Curr. Opin. phosphoglycerate kinase from Thermotoga maritima reveals the Struct. Biol. 2, 61–67. catalytic mechanism and determinants of thermal stability. Structure 5, 33. Saraste, M., Sibbald, P.R. & Wittinghofer, A. (1990). The P-loop — a 1475–1483. common motif in ATP- and GTP-binding proteins. Trends Biochem. 10. Larsen, T.M., Benning, M.M., Wesenberg, G.E., Rayment, I. & Reed, G.H. Sci. 15, 430–434. (1997). Ligand-induced domain movement in pyruvate kinase: structure 34. Schlichting, I. & Reinstein, J. (1997). Structures of active of the enzyme from rabbit muscle with Mg2+, K+, and L-phospholactate conformations of UMP kinase from Dictyostelium discoideum suggest at 2.7 Å resolution. Arch. Biochem. Biophys. 345, 199–206. phosphoryl transfer is associative. Biochemistry 36, 9290–9296. 11. Gerstein, M., Lesk, A.M. & Chothia, C. (1994). Structural mechanisms 35. Bossemeyer, D. (1994). The glycine-rich sequence of protein kinases: for domain movements in proteins. Biochemistry 33, 6739–6749. a multifunctional element. Trends Biochem. Sci. 19, 201–205. Minireview Enzyme-catalyzed phosphoryl transfer Matte, Tari and Delbaere 419

36. Fritz-Wolf, K., Schnyder, T., Wallimann, T. & Kabsch, W. (1996). Structure of mitochondrial . Nature 381, 341–345. 37. Kobayashi, N. & Go, N. (1997). ATP binding proteins with different folds share a common ATP-binding structural motif. Nat. Struct. Biol. 4, 6–7. 38. Kobayashi, N. & Go, N. (1997). A method to search for similar protein local structures at ligand binding sites and its application to adenine recognition. Eur. Biophys. J. 26, 135–144. 39. Traut, T.W. (1994). The functions and consensus motifs of nine types of peptide sequences that form different types of nucleotide-binding sites. Eur. J. Biochem. 222, 9–19. 40. Herschlag, D. & Jencks, W.P. (1990). Catalysis of the hydrolysis of phosphorylated pyridines by Mg(OH)+: a possible model for enzymatic phosphoryl transfer. Biochemistry 29, 5172–5179. 41. Admiraal, S.J. & Herschlag, D. (1995). Mapping the transition state for ATP hydrolysis: implications for enzymatic catalysis. Chem. Biol. 2, 729–739. 42. Maegley, K.A., Admiraal, S.J. & Herschlag, D. (1996). Ras-catalysed hydrolysis of GTP: a new perspective from model studies. Proc. Natl. Acad. Sci. USA 93, 8160–8166. 43. Hassett, A., Blättler, W. & Knowles, J.R. (1982). Pyruvate kinase: is the mechanism of phosphotransfer associative or dissociative? Biochemistry 21, 6335–6340. 44. Peliska, J.A. & O’Leary, M.H. (1991). Sulfuryl transfer catalyzed by phosphokinases. Biochemistry 30, 1049–1057. 45. Jones, J.P., Weiss, P.M. & Cleland, W.W. (1991). Secondary 18O isotope effects for hexokinase-catalyzed phosphoryl transfer from ATP. Biochemistry 30, 3634–3639. 46. Moréra, S., Chiadmi, M., LeBras, G., Lascu, I. & Janin, J. (1995). Mechanism of phosphate transfer by nucleoside diphosphate kinase: X-ray structures of the phosphohistidine intermediate of the enzymes from Drosophila and Dictyostelium. Biochemistry 34, 11062–11070. 47. Müller-Dieckmann, H.-J. & Schulz, G.E. (1994). The structure of uridylate kinase with its substrates, showing the transition state geometry. J. Mol. Biol. 236, 361–367. 48. Abele, U. & Schulz, G.E. (1995). High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer. Protein Sci. 4, 1262–1271. 49. Antonny, B. & Chabre, M. (1992). Characterization of the aluminum and beryllium fluoride species which activate transducin. Analysis of the binding and dissociation kinetics. J. Biol. Chem. 267, 6710–6718. 50. Xu, Y.-W., Moréra, S., Janin, J. & Cherfils, J. (1997). AlF3 mimics the transition state of protein phosphorylation in the crystal structure of nucleoside diphosphate kinase and MgADP. Proc. Natl. Acad. Sci. USA 94, 3579–3583. 51. Scheffzek, K., et al., & Wittinghofer, A. (1997). The Ras–RasGAP complex: structural basis for GTPase activation and its loss in oncogenic ras mutants. Science 277, 333–338. 52. Hollfelder, F. & Herschlag, D. (1995). The nature of the transition state for enzyme-catalyzed phosphoryl transfer. Hydrolysis of O-aryl phosphothioates by . Biochemistry 34, 12255–12264.