Crystal Structures of Human Pantothenate Kinases - The Journal of ...

THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 282, NO. 38, pp. 27984 –27993, September 21, 2007 © 2007 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in the U.S.A.

Crystal Structures of Human Pantothenate Kinases INSIGHTS INTO ALLOSTERIC REGULATION AND MUTATIONS LINKED TO A NEURODEGENERATION DISORDER *□ S

Received for publication, March 5, 2007, and in revised form, July 12, 2007 Published, JBC Papers in Press, July 13, 2007, DOI 10.1074/jbc.M701915200

Bum Soo Hong‡, Guillermo Senisterra‡, Wael M. Rabeh‡, Masoud Vedadi‡, Roberta Leonardi§, Yong-Mei Zhang§, Charles O. Rock§, Suzanne Jackowski§, and Hee-Won Park‡¶1 From the ‡Structural Genomics Consortium and ¶Department of Pharmacology, University of Toronto, Toronto, Ontario M5G 1L5, Canada and the §Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105-2794 Pantothenate kinase (PanK) catalyzes the first step in CoA biosynthesis and there are three human genes that express four isoforms with highly conserved catalytic core domains. Here we report the homodimeric structures of the catalytic cores of PanK1␣ and PanK3 in complex with acetyl-CoA, a feedback inhibitor. Each monomer adopts a fold of the actin kinase superfamily and the inhibitor-bound structures explain the basis for the allosteric regulation by CoA thioesters. These structures also provide an opportunity to investigate the structural effects of the PanK2 mutations that have been implicated in neurodegeneration. Biochemical and thermodynamic analyses of the PanK3 mutant proteins corresponding to PanK2 mutations show that mutant proteins with compromised activities and/or stabilities correlate with a higher incidence of the early onset of disease.

Pantothenate kinase (PanK)2 is the first and rate-limiting enzyme in the CoA biosynthetic pathway, which catalyzes the phosphorylation of vitamin B5, pantothenate (1). In human, there are three genes that express four catalytically active PanK isoforms. PanK1␣ and PanK1␤ arise from the PANK1 gene through the use of alternate initiating exons (2). PANK2 encodes a protein that is processed twice and localizes to the

* This

work was supported by the Structural Genomics Consortium with funds from Genome Canada through the Ontario Genomics Institute, the Canadian Institutes for Health Research, the Canada Foundation for Innovation, the Ontario Research and Development Challenge Fund, the Ontario Innovation Trust, the Wellcome Trust, GlaxoSmithKline, the Knut and Alice Wallenberg Foundation, Vinnova, the Swedish Foundation for Strategic Research, National Institutes of Health Grants GM62896 and GM34496, Cancer Center (CORE) Support Grant CA21765, and the American Lebanese Syrian Associated Charities. Use of the Advanced Photon Source was supported by the United States Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract DE-AC0206CH11357. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. □ S The on-line version of this article (available at http://www.jbc.org) contains supplemental Figs. S1–S4 and Table S1. The atomic coordinates and structure factors (code 2I7N and 2I7P) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/). 1 To whom correspondence may be addressed. Tel.: 416-946-3867; Fax: 416946-0880; E-mail: [email protected]. 2 The abbreviations used are: PanK, pantothenate kinase; PKAN, PanK-associated neurodegeneration; Pan, pantothenate; SaPanK, Staphylococcus aureus PanK; ITA, isothermal aggregation; AMP-PNP, adenosine 5⬘-(␤,␥-imido)triphosphate.

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mitochondria (3, 4) and PANK3 encodes a single cytosolic isoform (5). All of these PanK isoforms share a common, highly homologous catalytic core that is composed of about 355 residues (e.g. the identity of ⬃83%). PanK1␤ and PanK3 consist of the catalytic core alone, whereas PanK1␣ has a feedback regulatory domain in an amino-terminal extension (2). The NH2terminal domain of PanK2 includes two mitochondrial targeting signals, which are removed proteolytically concomitant with its mitochondrial localization (3, 6). In addition, PANK4 encodes a protein with sequence similarity to the other PanKs, but it lacks an essential catalytic glutamate for enzyme activity and has a long carboxyl-terminal extension of unknown function (3). Mutations in PANK2 have been linked to the inherited pantothenate kinase-associated neurodegeneration (PKAN) (7), which constitutes a subset of neurodegeneration with brain iron accumulation, formerly known as Hallervorden-Spatz syndrome (8). Patients with PKAN exhibit motor symptoms, such as dystonia, dysarthria, intellectual impairment, and gait disturbance (9) and early onset patients have rapidly progressive disease, whereas later onset patients have a slowly progressive, atypical disease (9, 10). The reason for brain iron accumulation in PKAN is still unknown. A current hypothesis of PKAN pathogenesis states that PANK2 mutations lead to a loss of PanK2 function and reduced phosphopantothenate, resulting in the accumulation of cysteine-containing molecules and CoA deficiency (6, 7). These cysteine-containing substrates may undergo rapid autoxidation in the presence of iron, leading to free radical generation and cell damage (6, 7). PANK2 mutations are clustered in the catalytic core domain, and insertion, deletion, and frameshift mutations in the PANK2 gene are linked clinically to early onset disease (10), indicating that null mutants of PanK2 lead to rapidly progressive PKAN. In contrast, the missense mutations have mixed early and late onset patterns (10), and a set of missense mutant proteins expressed in transiently transfected cells are active (4, 11), suggesting that defects unrelated to catalysis contribute to PKAN disease. A common feature of the PanK isoforms is that they are feedback inhibited by CoA and its thioesters. This regulation is a primary mechanism that controls PanK activity and hence the intracellular CoA level (2, 5, 12). Recent biochemical data show that acetyl-CoA is a more potent feedback inhibitor than free CoA for mouse PanKs (5, 11). Structural studies on PanK have been reported only in bacterial orthologs (13–17). The crystal structures of Escherichia coli PanK reveal why its activity, VOLUME 282 • NUMBER 38 • SEPTEMBER 21, 2007

Structures of Human Pantothenate Kinases unlike mouse PanKs, is more potently inhibited by free CoA, (13, 14). Staphylococcus aureus PanK (SaPanK) is the most similar in sequence to the mammalian PanK catalytic core (e.g. the identity of 23%), but is refractory to feedback regulation by CoA (17, 18). Due to the low sequence homology, the structural interpretation of the disease-causing human PanK2 mutations using the SaPanK model is limited to three missense mutations that directly affect the active site (17). We have determined the homodimeric structures of the catalytic cores of human PanK1␣ and PanK3 in complex with acetyl-CoA. These crystallographic data provide the first look at the structures of metazoan PanKs and their allosteric regulation. The high degree of similarity between human PanK3 and PanK2 allows an analysis of the mutations associated with PKAN. PanK2 missense mutations mapped onto the active site, dimerization interface, and protein interior tend to be associated with the early onset of PKAN phenotypes and their corresponding PanK3 mutant proteins show PanK inactivation and destabilization. On the other hand, mutations of surface residues have less severe effects on enzyme function and correlate with the mixed early and late onsets of disease.

EXPERIMENTAL PROCEDURES Protein Expression and Purification—The genes encoding the catalytic core domains of human PanK1␣ (residues 231– 597, abbreviated PanK1 below) and PanK3 (residues 12–368) were amplified using PCR and cloned into the expression vector pET28a to obtain NH2-terminal His6 tag fusion proteins. E. coli BL21(DE3) (Stratagene) was transformed with the resulting plasmids and both recombinant PanK1 and PanK3 proteins were overexpressed upon 1.0 mM isopropyl 1-thio-␤-D-galactopyranoside induction for 18 h at 18 °C. The proteins were purified using nickel-nitrilotriacetic acid affinity and Superdex 200 (GE Healthcare) gel-filtration columns. Purified PanK1 and PanK3 samples were concentrated to 25 and 30 mg/ml, respectively, and stored at ⫺80 °C in the gel filtration buffer (20 mM Tris-HCl, pH 8.0, 200 mM NaCl, 10 mM dithiothreitol). Crystallization—PanK proteins were crystallized using the sitting drop vapor diffusion method at 18 °C. To achieve full occupancy of bound ligands, the proteins were mixed with 5-fold molar excess of an ATP analogue AMP-PNP or acetylCoA. The mixtures were incubated overnight at 4 °C. Equal volumes of protein solution and reservoir solution were combined for crystallization. Crystals of PanK1 were grown at 0.1 M Na-Hepes (pH 7.5), 28% PEG400, 0.2 M CaCl2, and 0.02 M tris(2carboxyethyl) phosphine hydrochloride-HCl, and PanK3 was crystallized in 0.1 M Tris-HCl (pH 8.5), 16% PEG3350, 0.2 M ammonium citrate, and 0.02 M octaethyleneglycol dodecyl ether (C12E8). The mercury derivatives were obtained by soaking PanK1 crystals in the reservoir solution with 5 mM ethylmercury thiosalicylate overnight. All crystals were cryoprotected in the 50:50 mixture of Paratone-N and mineral oil, and flash-frozen in liquid nitrogen. The diffraction quality crystals of PanK1 were obtained in the presence of acetyl-CoA. Although AMP-PNP was added for the crystallization of PanK3, we found acetyl-CoA molecules in the structure that co-purified with PanK3. Data Collection and Structure Determination—Diffraction data were collected on beamline 19-BM at the Advanced PhoSEPTEMBER 21, 2007 • VOLUME 282 • NUMBER 38

ton Source, running at 100 K and processed using the HKL2000 program package (19). The program SOLVE (20) was used to locate four mercury sites and to calculate initial phases of PanK1 and the program RESOLVE (21) to improve the initial phases. The model of PanK1 was completed in several repetitions of manual building with the program O (22). The structure of PanK3 was solved by the molecular replacement method using the program MOLREP in the CCP4 package (23) and the PanK1 structure as a search model, and built using the program O (22). Finally, both PanK structures were refined with the program REFMAC5 (24). The crystals of PanK1 contained a dimer in the asymmetric unit and the two monomers were related by noncrystallographic 2-fold symmetry. In PanK3, two dimers were in the asymmetric unit. A dimer state is the most common functional organization for PanK proteins (4, 5, 25). Data collection and refinement statistics are given in Table 1. Site-directed Mutagenesis of PanK3—Based on the PanK2 mutations identified in PKAN patients (10), site-directed mutagenesis in PanK3 was accomplished using the Stratagene QuikChange kit (Stratagene). Prior to protein expression, the sequences of all mutations were verified by sequencing, and each mutant protein was purified as described for the wild-type protein, except the concentration of dithiothreitol was 1.0 mM. PanK Activity Assay—The effect of acetyl-CoA on the PanK1␣ and PanK3 Km values for ATP was investigated by using the assay previously described (2, 12). The standard reaction mixture contained 180 ␮M D-[1-14C]pantothenate (Amersham Biosciences), 10 mM MgCl2, 0.1 M Tris-HCl (pH 7.5), 200 ng of PanK1␣ or 100 ng of PanK3 and increasing concentrations of ATP and acetyl-CoA, as indicated. The mixture was incubated at 37 °C for 10 min and the radioactive product was quantitated by scintillation counting as described previously (11). Activities of PanK3 mutant proteins were compared with the wild-type using the standard pantothenate kinase assay (11). Briefly, the reaction mixture contained 90 ␮M D-[114 C]pantothenate, 2.5 mM ATP, 10 mM MgCl2, 0.1 M Tris-HCl (pH 7.5), and 100 ng of purified protein, and assayed as described above. Relative activities of the mutant proteins were checked three times and these data were combined. UV-visible Spectra and Mass Spectrometry—UV-visible spectra of PanK3 wild-type and mutant proteins (1 mg/ml in 10 mM Tris-HCl (pH 8.0), 50 mM NaCl, 0.5 mM EDTA, 0.5 mM dithiothreitol, and 50% (v/v) glycerol) were recorded as described previously (27). The supernatant (100 ␮l) from a heat-denatured sample of PanK3 (1.8 mg/ml in 50 mM ammonium acetate, pH 7.0) was desalted on a C-8 MicroTip column (Harvard Apparatus), washed with water, and the proteinbound small molecules were eluted with methanol (100 ␮l), dried under N2 flow, and resuspended in methanol:water (1:1, v/v, 10 ␮l). Mass spectrometry analysis was performed using a FinniganTM TSQ威 QuantumTM (Thermo Electron Corporation, San Jose, CA) triple quadrupole mass spectrometer equipped with the nanospray ion source. Stability Studies by Differential Static Light Scattering—The thermostabilities of PanK3 and its mutant proteins were studied using differential static light scattering (28, 29), monitoring protein stability by its aggregation properties. Protein samples at 0.2 mg/ml were heated from 25 to 80 °C at a rate of 1 °C/min JOURNAL OF BIOLOGICAL CHEMISTRY

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Structures of Human Pantothenate Kinases TABLE 1 Crystallographic data and refinement statistics PANK1

Crystal

Hg for MAD

Native

PANK3, native

Space group Unit cell parameters (Å)

Peak P63 a ⫽ b ⫽ 93.4 c ⫽ 198.0

Edge P63 a ⫽ b ⫽ 93.5 c ⫽ 198.3

P63 a ⫽ b ⫽ 92.9 c ⫽ 197.7

Wavelength (Å) Resolution range (Å) Completeness (%)a Total no. of reflections No. of unique reflections Rsym (%)b

1.00510 50–2.5 99.7 (100) 2,304,183 33,600 7.6 (10.5)

1.00900 50–2.5 99.7 (100) 2,360,276 336,756 6.7 (12.5)

1.54178 50–1.9 99.5 (98.9) 1,660,535 75,175 6.7 (61)

P21 a ⫽ 56.7 b ⫽ 180.1 c ⫽ 77.7 1.00003 50–2.05 98.4 (90.5) 1,295,364 96,048 8.8 (52.2)

50–1.9 22.2 (24) 24.3 (31.8)

50–2.05 21.1 (27.8) 25.4 (35.8)

5,143 58 252

10,967 116 715

0.007 1.5

0.006 1.2

Phasing Resolution range (Å) Mean figure of merit Mean figure of merit after density modifiction

42–3.0 0.68 0.76

Refinement statistics Resolution range (Å) Rwork (%)c Rfree (%)d No. of atoms Protein Ligand/ion Water Root mean square deviations from ideality Bond lengths (Å) Bond angles ( degrees ) Ramachandran plot Most favored (%) Additional allowed (%) Generously allowed (%)

90.1 9.2 0.7

90.5 8.9 0.6

a

Values in parentheses are for the highest resolution shell. Rsym ⫽ 兺兩(I ⫺ 具I典)兩I兺(I), where I is the observed intensity. c Rwork ⫽ 兺储Fobs兩 ⫺ 兩 Fcalc储兺兩Fobs兩, where 兩Fobs兩 and 兩Fcalc兩 are observed and calculated structured factor amplitude. d The Rfree value was calculated with a random 5% subset of all reflections excluded from refinement. b

in clear bottom 384-well plates (Nunc) in 50 ␮l of buffer (100 mM Hepes, 150 mM NaCl, pH 7.5). Protein aggregation was measured by recording the scattered light using a CCD camera and taking images of the plate every 0.5 °C. The pixels intensities in a preselected region of each well were integrated using proprietary software to generate a value representative of the total amount of scattered light in that region. These intensities were plotted against temperature for each sample well and fitted to Equation 1 as described by Matulis et al. (30), I ⫽ If ⫹

冉

Io ⫺ If 1 ⫹ e 共 ⫺ ⌬H/R兲共1/T

冋冉冉冊

⫺ 1/T agg兲 ⫹ ⌬Cp ln

T Tagg

⫹

Tagg ⫺ 1 T

冊册

冊

(Eq. 1)

where Io and If are the intensities of light scattered by the protein before and after denaturation, ⌬H is the enthalpy of unfolding, R is the general gas constant, Tagg is the temperature of aggregation that represents the melting temperature, and ⌬Cp is the heat capacity difference between the unfolded and folded states of the protein. ⌬Cp of 4.93 kcal/mol was calculated based on the protein sequence and was used in all subsequence calculations (31). The free energy difference ⌬⌬G between the wildtype and each mutant protein at the temperature of aggregation of the wild-type was calculated using Equation 2, ⌬⌬Gm(Twt) ⫽ ⌬Hm ⫺ [Twt/Tm]䡠⌬Hm

(Eq. 2)

where ⌬⌬Gm(Twt) is the denaturation free energy difference


between the wild-type and mutant PanK3, Twt and Tm are the aggregation temperatures of the wild-type and mutant proteins, respectively. Stability Studies by Isothermal Aggregation (ITA)—Isothermal aggregation was measured at 37 °C. Protein samples at 0.2 mg/ml were incubated at 37 °C in clear bottom 384-well plates (Nunc) in 50 ␮l of buffer (100 mM Hepes, 150 mM NaCl, pH 7.5). Protein aggregation was monitored by detecting the scattered light by taking images every 30 s using a CCD camera for 2 h. Images were analyzed and the intensities were plotted versus time. All curves were normalized to compensate for small differences in initial intensities. The time it takes to have 50% of the protein in the aggregation state, here on, is termed ITA50. Each experiment was repeated 5 times and the average has been reported here.

RESULTS Overall Structure Description The PanK1 and PanK3 proteins we crystallized represent the catalytic core domain, which is highly conserved in all human PanK isoforms. The identity between the catalytic core domains of the two isoforms is ⬃84% (ClustalW 1.7). The overall monomer fold places the human PanKs in the actin fold protein kinase superfamily (32), and contains two domains (Fig. 1A). The A domain consists of a six-stranded ␤-sheet (strands Ab1–Ab6) flanked by five helices (Ah1–Ah3 on one side and Ah4 and Ah11 on the other side) and a glycine-rich loop, characteristic of many nucleotide-binding sites (33, 34), lies VOLUME 282 • NUMBER 38 • SEPTEMBER 21, 2007

Structures of Human Pantothenate Kinases S2A). The center of the four-helix bundle is lined by non-polar residues forming a compact hydrophobic core. The narrow COOH-terminal ends of helices Bh9 and Bh9⬘ are held together by van der Waals interactions between Val304 and Met307 of each monomer, and are capped by Asn311 and Asn311⬘ which face each other. The middle of helices Bh9 and Bh9⬘ is attached by both direct and water-mediated hydrogen bonds between Asn300 and Asn300⬘. Additional van der Waals interactions exist between Bh5 of one monomer and the extended loop of the second monomer contributing to the stabilization of the PanK dimer (supplemental Fig. S2B). The Acetyl-CoA Binding Site In both PanK1 and PanK3 structures, the acetyl pantetheine diphosphate moiety of acetyl-CoA is bound parallel to the ␤ strands of the B domain of one monomer and covered on the other side by the FIGURE 1. Overall view of the structure of human PanK3. A, stereo view of a ribbon representation of the PanK3 monomer structure. The secondary structure elements (h for helices and b for sheets) start with prefixes extended loop of the second monoA and B to indicate A and B domains, respectively. The extended loop region and the predicted ATP binding site mer (Fig. 2A). The main interac(arrow) are indicated. B, ribbon representation of the PanK3 dimer structure. Two molecules in the PanK3 dimer are in green and yellow, respectively. Acetyl-CoA is in ball-and-stick representation. Helix Bh9 of the B domain tions of acetyl-CoA with PanKs of the first monomer and helix Bh9⬘ of the B⬘ domain of the second monomer that form the dimerization occur via the acetyldiphosphointerface are labeled. All the figures were generated by PyMol (pymol.sourceforge.net). pantetheine moiety (Fig. 2B). The 3⬘-phosphoadenonsine moiety is between strands Ab1 and Ab2. The B domain consists of a nine- poorly defined in the electron density map, suggesting that it is stranded ␤-sheet (strands Bb7–Bb15). One side of this sheet is disordered and thus not included in the final PanK structures. flanked by six helices (Bh5–Bh10) and an extended loop region Residues lining the binding site of the acetyldiphosphopantethbetween helices Bh6 and Bh9, whereas the other side faces the A eine are identical in both the PanK structures, with the excepdomain. The B domains of PanK1 and PanK3 contain an exten- tion of residues 266 and 340 involved in hydrophobic interacsive dimerization interface. Whereas the overall root mean tions (Fig. 2B). The acetyldiphosphopantetheine moiety forms square deviation of the two PanK structures including both A direct or water-mediated hydrogen bonds and van der Waals and B domains was ⬃1.5 Å for the C␣ atoms, the root mean interactions with the protein core. The polar residues involved square deviation of the A domain was 1.4 Å, and the root mean in hydrogen bonds are from the ␤ strands of one monomer square deviation of the B domain was 0.85 Å, suggesting that (Bb9 –Bb11) and the non-polar residues involved in van der the B domains are structurally more conserved than the A Waals interactions are contributed by the extended loop and domains (supplemental Fig. S1). As the A domain in the PanK1 Bh10⬘ of the second monomer (Fig. 2A). Acetyl-CoA was very model was partly incomplete due to poor electron density (sup- tightly bound to PanK3 in the structure, consistent with the low plemental Fig. S1), the PanK3 structure was used for “Results ” IC50 value for acetyl-CoA inhibition of the enzyme (5). and “Discussion, ” and only its differences from PanK1 were Predicted Binding Sites for ATP and Pantothenate pointed out. The ATP binding site of PanK3 was modeled on the basis of Dimerization Interface its structural similarity to the SaPanK䡠AMP-PNP complex The major portion of the dimerization interface is composed (Protein Data Bank code 2EWS) (17) and the location of the of two long helices, Bh9 and Bh9⬘ from each monomer, which conserved glycine-rich loop (Fig. 3A). Superposition of the B interact with each other in parallel resulting in a V-shaped con- domain of PanK3 and the corresponding domain of the formation (Fig. 1B and supplemental Fig. S2A). Helices Bh9 and SaPanK䡠AMP-PNP complex placed the ATP molecule between Bh9⬘ widen at their NH2-terminal ends and form a four-helix the two domains of the human PanKs. The two domains of bundle with two short helices Bh5 and Bh5⬘ (supplemental Fig. PanK3 and also PanK1 were in an “open” conformation comSEPTEMBER 21, 2007 • VOLUME 282 • NUMBER 38

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FIGURE 2. Acetyl-CoA interactions with human PanK3. A, stereo view of a Fo ⫺ Fc difference map of acetyl-CoA (the acetyl-pantetheine moiety, see “Results”) shown in black stick representation. The difference map was calculated before introducing the molecule acetyl-CoA and contoured at 2.5 ␴. Two PanK3 monomers forming the acetyl-CoA binding site are in green and yellow, respectively. A single prime superscript indicates the secondary structure elements from the second monomer. B, schematic representation of the acetyl-CoA interactions with PanK3. Blue dotted lines indicate hydrogen bonds, whereas red dotted semicircles mark hydrophobic interactions. The residues that form the hydrogen bonds to acetyl-CoA are boxed. S and M superscripts indicate the acetyl-CoA interactions with the side chain and main chain of residues, respectively. One water molecule (W) is displayed in the red sphere. The sequence differences between PanK3 and PanK1 are given in parentheses (e.g. Trp266 and Tyr340 of PanK3 are replaced by serine and phenylalanine in PanK1, respectively).

pared with the “closed ” conformation SaPanK䡠AMP-PNP (Fig. 3A). The binding of the acetyl-CoA kept PanK in the open conformation, characteristic of the ligand-free structures of actinfold proteins (32). Acetyl-CoA was a competitive inhibitor of both PanK1 and PanK3 (Fig. 3, B and C), suggesting that the binding of acetyl-CoA interfered with the ATP binding by stabilizing the open conformation. Based on the superimposed structures of PanK3䡠acetyl-CoA and SaPanK䡠AMP-PNP, the ␣,␤-phosphates of acetyl-CoA and the ␤,␥-phosphates of ATP occupied the same space (Fig. 3A), explaining the competitive nature of acetyl-CoA and ATP for PanK. Also, we found that a high proportion of purified PanK3 was bound to acetyl-CoA. Heat denaturation of the protein released the bound compound into the supernatant, and analysis of this supernatant by mass spectrometry identified it as acetyl-CoA (Fig. 3D). This indicates that acetylCoA remained bound to PanK3 during purification. The Pan binding site was predicted on the basis of the location of bound acetyl-CoA in PanK3. The same residues lining


the binding pocket for the Pan moiety of acetyl-CoA (Fig. 2B) were considered for the binding of Pan. A key residue was Arg207 that formed a salt bridge to the carboxamide group of the Pan moiety of acetylCoA (the carboxyl group of Pan) (Fig. 2B). This salt bridge interaction would anchor one end of Pan. A similar salt bridge interaction was observed in the Pseudomonas aeruginosa PanK structure (17). However, Glu138, another key residue, predicted to act as a general base for the nucleophilic activation of the hydroxyl group of Pan in SaPanK (17), was not located adjacent to the 4⬘-hydroxyl group of Pan (data not shown), suggesting that the enzyme exists in a catalytically inactive state. This finding is consistent with the idea that the acetyl-CoA-bound PanK3 structure adopts the open conformation (see above). Therefore, a switch to the closed conformation by the binding to ATP and/or Pan is required for the nucleophilic activation of the OH group of Pan by Glu138. Crystallographic Mapping of Missense Mutations Associated with PKAN Disease

The sequence similarity in the catalytic core domains of PanK3 and PanK2 allowed mapping of the PanK2 missense mutations (10) onto the PanK3 structure (Fig. 4A) and we correlated the locations of the missense mutations with their biochemical and disease phenotypes (Table 2). The mutations were grouped into three categories. Active Site Mutations—Two PanK2 mutations (G219V and G521R) mapped to the ATP binding site and of these, G521R is most frequently observed in PKAN patients (10). Gly321 (Gly521 of PanK2) was located in the loop between Bb14 and Bh10 on one side of the ATP binding site, whereas Gly19 (Gly219 of PanK2) formed part of the glycine-rich loop (supplemental Fig. S3A). These glycine residues create space for the docking of the ATP phosphates, and the introduction of a side chain by mutation, especially a bulky one, was predicted to prevent proper ATP binding. A previous study of both mutations in PanK2 has shown that these mutant proteins were catalytically inactive, and the PanK2-(G521R) failed to properly fold (11). Mutations at the Dimer Interface and Protein Interior—The PanK3 structure placed eight PanK2 missense mutations (L413P, D447N, S471N, I497T, N500I, I501T, A509V, and VOLUME 282 • NUMBER 38 • SEPTEMBER 21, 2007

Structures of Human Pantothenate Kinases located in the protein interior (Fig. 4A) and the corresponding residues (Leu82, Ala198, and Leu363) in PanK3 were involved in the hydrophobic interactions with surrounding nonpolar residues. Mutations on the Surface of PanK—Fifteen PanK2 mutations were located on the surface of the PanK3 structure with their side chains exposed to solvent (Fig. 4B). Most notable was PanK2-(T528M), the second most common mutation in PKAN disease (10, 35). Thr528 of PanK2 was equivalent to Thr328 of PanK3 and Met553 of PanK1, which was located at the NH2 terminus of helix Bh10 (supplemental Fig. S3D). Based on our sequence alignment (data not shown) and both PanK structures, the side chain hydroxyl group of Thr528 in PanK2 was predicted to form a hydrogen bond to Arg532 and PanK2-(T528M) was predicted to break this interaction as shown in wild-type PanK1. The side chain of Lys332 in PanK3 formed water-mediated hydrogen bonds to residues in the loop between Bb7 and Bb8 (supplemental Fig. S3D), which could be achieved by the corresponding Arg532 in PanK2. Interestingly, FIGURE 3. The putative binding site of ATP. A, structural superposition of the glycine-rich loops of this arginine mutation, PanK2PanK3䡠acetyl-CoA (green) and SaPanK䡠AMP-PNP (gray) (PDB entry 2EWS). AMP-PNP is in pink and acetyl- (R532W), was found in PKAN CoA in cyan. Conserved residues of the glycine-rich loop in PanK3 are marked with an asterisk. An arrow patients, supporting the idea that the indicates the structural transition from open to closed conformations of the glycine-rich loop after ATP 528 532 interaction is imporbinding. B and C, inhibitions of PanK1 and PanK3 by acetyl-CoA. The Km values of PanK1 and PanK3 for ATP Thr –Arg were determined in the presence of increasing acetyl-CoA concentrations as described under “Experi- tant in positioning the Bb7–Bb8 loop mental Procedures.” Double reciprocal plots of the velocity versus the ATP concentration reveal that acetyl-CoA is a competitive inhibitor for both PanK1 (B) and PanK3 (C). D, electrospray-mass spectrometry for some physiological function of spectrum of the supernatant from a heat-denatured sample of PanK3. The spectrum reveals the presence PanK2. of peaks at m/z 403.79 and 808.18 corresponding to the acetyl-CoA [M ⫺ 2H]2⫺ and [M ⫺ H]⫺ ions, Mutations at Arg64, Arg78, Arg86, respectively. Ser151, and Asn155 of PanK3 (i.e. PanK2-(R264W), -(R278L or C), N511D) at the dimer interface (Fig. 4A). Of these, Leu213 -(R286C/S351P), and -(N355S)) were predicted to disrupt salt (Leu413 of PanK2) made van der Waals interactions with non- bridges or hydrogen bonds with surrounding residues, also conpolar residues (supplemental Fig. S3B), and Asp247, Ser271, served between PanK3 and PanK2 (data not shown). Cys228 of Asn300, and Asn311 (Asp447, Ser471, Asn500, and Asn511 of PanK3 (Cys428 of PanK2) was located on the protein surface but its PanK2) formed direct or water-mediated hydrogen bonds to side chain pointed to the protein core (Fig. 4B). Finally, the PanK3 helix Bb9⬘ of the second monomer (supplemental Figs. S2A and structure indicated that the side chains of five residues, Thr34, S3, B and C). On the other hand, Ile297, Ile301, and Ala309 (Ile497, Arg49, Glu122, Thr127, and Asn204, corresponding to six PanK2 Ile501, and Ala509 of PanK2) were indirectly involved in PanK3 mutations, T234A, R249P, E322G or D, T327I, and N404I, were dimerization. Many water molecules were trapped at the dimer exposed to solvent with no other apparent interactions. interface and formed a network through the interaction with amino acid residues along the dimer interface (supplemental Biochemical and Thermodynamic Characterization of PanK3 Fig. S3, B and C). This network, conserved in both PanK1 and Mutant Proteins PanK3 structures, is considered to tighten the dimerization of We cloned, expressed, and purified 27 PanK3 mutant protwo monomers and the mutations at Asp247, Ser271, and Asn300 teins that correspond to the PanK2 missense mutations of PanK3 were predicted to perturb the ordered water mole- described above. The effects of these mutations on activity and cules. Three PanK2 mutations, L282V, A398T, and L563P, were stability of the protein were investigated using in vitro PanK SEPTEMBER 21, 2007 • VOLUME 282 • NUMBER 38


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Structures of Human Pantothenate Kinases (PanK2-(G219V)) had negligible activity (⬇1%) and its Tagg (36.7 °C) was lower than the wild-type (45.4 °C) with a significant destabilization energy of ⫺2.46 Kcal/mol (Table 2). PanK3-(G321R)(PanK2(G521R)) was insoluble and could not be studied with either technique. Of the dimer interface mutant proteins, L213P (PanK2-(L413P)) and N300I (PanK2-(N500I)), eluted as monomers by gel filtration chromatography, showed low Tagg values (36.9 and 36.6 °C) with ⌬⌬G values of ⫺3.32 and ⫺1.84 Kcal/mol, respectively, and they also exhibited compromised catalytic activities (Table 2). Three other PanK3 mutations along the dimer interface, D247N (PanK2(D447N)), S271N (PanK2-(S471N)), and I297T (PanK2-(I497T)) did not affect dimer assembly but significantly altered their enzymatic activities and thermostabilities. The other dimer interface mutant proteins, I301T (PanK2-(I501T)), A309V (PanK2(A509V)), and N311D (PanK2(N511D)) eluted as dimers and showed moderate protein destabilizations, and no significant changes in their activities relative to the wild-type (Fig. 4C). A mutation in the interior of PanK3, L363P (PanK2-(L563P)), exhibited complete insolubility in protein purification trial, whereas the other interior mutant protein, L82V (PanK2(L282V)) was soluble and displayed moderate destabilization with catalytic activity similar to the wild-type (Fig. 4C). Most of the surface mutations exhibited moderate or no significant reduction in their thermostability (Tagg) or activity (Fig. 4C). Of these, PanK3-(R64W) (PanK2-(R264W)) FIGURE 4. Mapping of PKAN-linked PanK2 mutations onto the PanK3 structure and characterization of was stable with a T agg value similar to PanK3 mutant proteins. A, stereo view of the PanK2 mutations mapped onto the PanK3 monomer structure. the wild-type and low ⌬⌬G (0.16 Each mutation site is marked as a red sphere. The locations of the mutation sites are labeled (a ⫽ ATP binding, d ⫽ dimerization interface, i ⫽ interior, and s ⫽ surface) and the top two frequently observed mutations in Kcal/mol), but the activity was PKAN patients are highlighted in yellow. B, PanK2 surface mutations mapped onto PanK3 dimer. The surface reduced to 36% of the wild-type. On mutation sites are shown in red. The inset shows close-up views of PanK3-(R64W), -(R86C), and -(C228Y) corresponding to PanK2-(R264W), -(R286C), and -(C428Y) with a 90° rotation. C, relative activities and thermody- the other hand, the Tagg values of namic characterizations of PanK3 mutant proteins corresponding to the PKAN-associated PanK2 mutations. the three other surface mutant proTop histogram (blue) shows the kinase activities of PanK3 mutant proteins relative to the wild-type. Each bar represents the mean of at least three independent measurements. Error bars show S.D. Bottom histogram (red) teins, R86C (PanK2-(R286C)), S151P indicates denaturation free energy differences (⌬⌬G) between wild-type PanK3 and its mutant proteins. SDS- (PanK2-(S351P)), and K332W (PanK2PAGE is shown between the two histograms. Insoluble mutant proteins are marked with an asterisk. (R532W)), decreased to ⬃40 °C with ⌬⌬G between ⫺0.9 and ⫺1.57 Kcal/ activity and thermostability assays (Fig. 4C, Table 2). The muta- mol; nevertheless, their activities were similar to that of the tions located at the ATP binding site severely affected the cat- wild-type (Table 2). These findings suggest that the effects of alytic activity and stability of the protein. PanK3-(G19V) these surface mutations are not always the same on both pro-


VOLUME 282 • NUMBER 38 • SEPTEMBER 21, 2007

Structures of Human Pantothenate Kinases TABLE 2 Enzyme activities and thermostabilities of PanK3 mutant proteins Mutations PanK3

PanK2

WT

Number of patienta

Relative activity

Tag

⌬⌬G

°C

Kcal/mol

45.4

0.0

100 ⫾ 2.3

100

PanK2b

PanK3

Early onset

Late onset

24

1 7

%

ATP binding G19V G321Rc

G219V G521R

36.7 NDd

⫺2.46 ND

1.4 ⫾ 1.2 ND

0.4 ⬍0.2

Dimerization domain L213P D247N S271N N300I I297T I301T A309V N311D

L413P D447N S471N N500I I497T I501T A509V N511D

36.9 36.6 36.1 36.6 37.7 41.1 42.2 40.5

⫺3.32 ⫺4.11 ⫺4.36 ⫺1.84 ⫺3.0 ⫺1.23 ⫺0.77 ⫺1.71

2.0 ⫾ 0.4 5.2 ⫾ 0.5 2.6 ⫾ 0.3 3.5 ⫾ 0.9 14.5 ⫾ 4.4 82.9 ⫾ 2.8 62.4 ⫾ 0.7 164.9 ⫾ 5.0

ND ND 16 3.9 ND ND 105 ND

1 1 3 2 1

Interior L82V A198Te L363Pc

L282V A398T L563P

42 ND ND

⫺0.81 ND ND

141.9 ⫾ 3.1 ND ND

ND ND ⬍0.2

1 1 1

Surface T34A R49P R64W R78L R78C R86C E122G E122D T127I S151P N155S N204I C228Y T328M K332Wf

T234A R249P R264W R278L R278C R286C E322G E322D T327I S351P N355S N404I C428Y T528M R532W

46.2 45.8 46 42.6 43 40.6 43.8 43.2 42.3 39.8 45 42.4 44.7 46.2 40.9

0.12 0.07 0.16 ⫺0.83 ⫺0.74 ⫺1.41 ⫺0.26 ⫺0.59 ⫺0.60 ⫺1.57 ⫺0.06 ⫺0.65 ⫺0.14 0.11 ⫺0.90

153.5 ⫾ 2.0 122.9 ⫾ 0.4 35.7 ⫾ 0.7 172.5 ⫾ 4.3 184.9 ⫾ 0.8 154.9 ⫾ 1.7 138 ⫾ 6.6 149.6 ⫾ 3.4 112 ⫾ 3.1 103.7 ⫾ 8.1 138.5 ⫾ 7.0 159.4 ⫾ 7.9 147.4 ⫾ 11 162.1 ⫾ 7.9 79.7 ⫾ 1.7

112 ND 58 ND ND 176 ND ND 91 78 ND 83 ND 146 95

1 2 1

2 1 2 1 2 1

1 2 1

2 2 1 3 1 3 2

7

a

The number of early and late onset patients for PanK2 mutation is taken from Hayflick et al. (10). The value of activity for each PanK2 mutant protein is taken from Zhang et al. (11). c Insoluble mutant protein. d ND, not determined. e Mutant not tested. f Lys332 of PanK3 corresponds to Arg532 of PanK2. b

tein thermostability and activity. The other 11 surface mutations including T328M (PanK2-(T528M)) displayed moderate or no protein destabilization and their activities were similar to the wild-type. Some of the surface mutations such as PanK3-(T34A), PanK3-(R49P), PanK3-(R64W), PanK3-(N155S), PanK3(C228Y), and PanK3-(T328M) had only a negligible effect on the stability of the protein (⌬Tagg ⬍ 2 °C) (Table 2), which is within the experimental error of differential static light scattering. We performed further tests with these mutant proteins by ITA, a more sensitive technique than differential static light scattering that monitors the aggregation of the proteins at constant temperature under a defined set of buffer conditions (36, 37). At 37 °C, the time required to reach 50% aggregation (ITA50) for wild-type PanK3 was 33.5 min, whereas PanK3(T328M) corresponding to PanK2-(T528M) was 25 min (supplemental Table S1). Most of the PanK3 surface mutant proteins aggregated more quickly than the wild-type protein (supplemental Table S1), suggesting that the mutations had reduced protein stability.

DISCUSSION PanK Regulation by Feedback Inhibition—Crystallographic identification of the acetyl-CoA binding sites of PanK1 and SEPTEMBER 21, 2007 • VOLUME 282 • NUMBER 38

PanK3 provides an explanation for the weaker inhibitory effects of CoA. CoA and its thioesters (acetyl-CoA, malonyl-CoA, and palmitoyl-CoA) inhibit PanKs, but they show different potencies for mammalian PanK isoforms (2, 5). CoA inhibits mouse PanK3 with a significantly higher IC50 than acetyl-CoA (5). Similarly, CoA inhibits mouse PanK1␣ with the IC50 of 80 ␮M, whereas acetyl-CoA has an IC50 of 5 ␮M (5). The structures of catalytic core domains of two PanK isoforms suggest that the lower potency of CoA, compared with its thioesters, is attributed to the lack of the thioester carbonyl oxygen that forms a hydrogen bond with the main chain amide of a valine (supplemental Fig. S4). Additionally, the binding pocket for the acetyl moiety of acetyl-CoA is partially exposed to solvent, providing the opening for longer chain acyl moieties to interact with the same site. The monomer folding and dimer assembly of human PanK catalytic core domains are similar to that of SaPanK (17). Unlike human PanKs, however, SaPanK is refractory to inhibition by CoA and its thioesters (18). Compared with the human PanK3 structure, SaPanK has two residues that line the acetylCoA pocket that would hinder the binding of feedback inhibitors (Ala337 of PanK3 versus Tyr240 of SaPanK and Trp341 of PanK3 versus Arg244 of SaPanK) (supplemental Fig. S4). The JOURNAL OF BIOLOGICAL CHEMISTRY

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Structures of Human Pantothenate Kinases substitution of alanine to a bulky residue, tyrosine, may cause steric hindrance for the binding of CoA and the substitution of tryptophan to arginine introduces a positive charge, disrupting the hydrophobic binding pocket for the sulfhydryl group of CoA or the acyl groups of the thioesters. These two residues in PanK3 are also conserved in the other PanK isoforms (supplemental Fig. S4). PanK2 Instability as a Determinant of PKAN—Structural analysis of the catalytic cores of PanK1 and PanK3 provides an opportunity to understand why many of the mutations that give rise to PKAN disease abolish the catalytic activity of PanK. Of the two mutations at the ATP-binding site, PanK3-(G19V) exhibits large reductions in both protein stability and enzymatic activity, and PanK3-(G321R) is insoluble (Fig. 4C). Low enzymatic activity, structural instability, and abnormal processing are observed with the corresponding human PanK2(G219V) and PanK2-(G521R) mutations (4, 11). Many of the inactivating mutations are located in the dimerization interface and require between ⫺0.77 and ⫺4.36 Kcal/mol less free energy than the wild-type to unfold. Five of eight dimerization mutations give rise to catalytically inactive proteins in vitro, although three dimerization mutations have a less severe effect on activity (Fig. 4C). Similarly, one of the three mutations in the inner protein core, PanK3-(L363P), is insoluble (data not shown). The corresponding PanK2-(L563P) mutant protein is catalytically inactive (11). Our findings on the activities of the PanK3 mutant proteins reflect data obtained with the authentic PanK2 protein (4, 11), supporting the close relationship between the structures of these proteins. These findings suggest that proper monomer folding and dimerization are critical for the stability of PanK3 and enzymatic activity. More than 80% of patients who have the PanK2 active site or dimerization mutations are linked to the clinically early onset phenotype (10) (Table 2), thus structural destabilization of monomers that cannot form dimers or improperly formed dimers appears as a major contributor to PKAN. The group of mutations that has confounded the field maps predominantly to the protein surface. Hydrophilic or charged residues are frequently substituted with hydrophobic residues (11 of 15 surface mutations), and these mutations do not result in the loss of PanK2 (11) or PanK3 catalytic activity and have ⌬⌬G values ⬍2 Kcal/mol in the PanK3 model (Table 2). Surface residues of globular proteins are mainly hydrophilic, and the stabilities of globular proteins are altered by changing surface residues involved in salt bridge or hydrogen bond interactions (39 –44). Substitutions of solvent-exposed hydrophilic residues to hydrophobic residues may locally disrupt the hydrophilicity of the protein (45), destabilizing protein conformation. Of 15 surface mutant proteins of PanK3, eight have moderate reductions (⌬Tagg ⬎ 2 °C) in the Tagg values and 14 are rapidly aggregated in vitro at 37 °C compared with wild-type, but retain activity (Table 2 and supplemental Table S1). It will be important to extend these experiments from the PanK3 model to actual PanK2 mutant proteins because the degree of destabilization by elimination of surface salt bridges is highly dependent on the context in which they occur, and there are 56 amino acid differences between PanK3 and PanK2 plus an additional 60-residue amino-terminal extension in PanK2 that interacts with the


catalytic core in an unknown way and may either positively or negatively affect the degree of protein destabilization by surface mutation changes. Kotzbauer et al. (4) examined the stability and processing of PanK2 mutant proteins in cultured cells. PanK2-(G521R) has a shorter half-life and is abnormally processed compared with wild-type, consistent with the compromised structural integrity of the corresponding PanK3 mutant protein. These data indicate that the other PanK2 mutant proteins that correspond to PanK3 mutant proteins that alter protein stability may have a shorter half-life in vivo than their wild-type counterpart, and perhaps explains why these mutations are associated with early onset of the disease. However, the surface mutations have modest effects on PanK3 stability and similar in vivo experiments with the PanK2-(T528M) and PanK2-(T234A) did not reveal any differences between these two mutants and the wild-type with respect to activity, stability, and processing (4). Our biophysical studies on the analogous PanK3 isoform may suggest that there may still be more subtle effects on stability than noted in these experiments, or that alternatively, the surface mutations may relate to compromising the binding of PanK2 to as yet unidentified protein partners or regulatory ligands. On the other hand, PanK2 is translocated into the mitochondria (3, 4) and mitochondria produce most of the reactive oxygen species (46), suggesting the damage of mitochondrial PanK2 by reactive oxygen species is possible. Hydrogen peroxide is one of the major reactive oxygen species in mitochondria and modifies sulfur-containing amino acids (26, 38). Some PanK2 surface mutant proteins such as PanK2-(R278C), -(R286C), and -(T528M) may be more susceptible to hydrogen peroxide modification than wild-type and when modified, enhance protein destabilization in mitochondria. In summary, we have presented the first structure of human PanK1 and PanK3 isoforms in complex with acetyl-CoA. The structures show a common architecture of the catalytic cores of human PanK isoforms and explain the allosteric regulation during CoA biosynthesis. Mapping of PanK2 mutations to the PanK3 structure and mutational studies on PanK3 isoform reveal that mutations at the ATP binding site, dimer interface and protein interior compromise their enzyme activities and stabilities and are mostly associated with the early onset of the PKAN phenotype, whereas surface mutations are catalytically active but show slight instabilities relative to the wild-type and are linked to the mixed onset of disease phenotype. These findings contribute to our understanding of the dysfunctional effects of polymorphic PanK2 mutations and help decipher the manner in which enzymatically active mutant proteins are linked to disease. Acknowledgments—We thank members of Structural Genomics Consortium, notably Louis Wang, Limin Shen, and Peter Loppnau for expert technical assistance and Wolfram Tempel for assistance with x-ray data collection. We thank Cheryl H. Arrowsmith and Jinrong Min for helpful discussions. We also thank the IMCA-CAT beamline staffs of APS for help during data collection.

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