Metal Specificity Is Correlated with Two Crucial Active Site Residues in Escherichia coli Alkaline Phosphatase,

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1 8378 Biochemistry 2005, 44, Metl Specificity Is Correlted with Two Crucil Active Site Residues in Escherichi coli Alkline Phosphtse, Jie Wng, Kimberly A. Stieglitz, nd Evn R. Kntrowitz* Deprtment of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Msschusetts ReceiVed Jnury 26, 2005; ReVised Mnuscript ReceiVed Mrch 18, 2005 ABSTRACT: Escherichi coli lkline phosphtse exhibits mximl ctivity when Zn 2+ fills the M1 nd M2 metl sites nd Mg 2+ fills the M3 metl site. When other metls replce the zinc nd mgnesium, the ctlytic efficiency is reduced by more thn 5000-fold. Alkline phosphtses from orgnisms such s Thermotog mritim nd Bcillus subtilis require coblt for mximl ctivity nd function poorly with zinc nd mgnesium. Previous studies hve shown tht the D153H lkline phosphtse exhibited very little ctivity in the presence of coblt, while the K328W nd especilly the D153H/K328W mutnt enzymes cn use coblt for ctlysis. To understnd the structurl bsis for the ltered metl specificity nd the bility of the D153H/K328W enzyme to utilize coblt for ctlysis, we determined the structures of the inctive wild-type E. coli enzyme with coblt (WT_Co) nd the structure of the ctive D153H/K328W enzyme with coblt (HW_Co). The structurl dt revel differences in the metl coordintion nd in the strength of the interction with the product phosphte (P i ). Since relese of P i is the slow step in the mechnism t lkline ph, the enhnced binding of P i in the WT_Co structure explins the observed decrese in ctivity, while the wekened binding of P i in the HW_Co structure explins the observed increse in ctivity. These ltertions in P i ffinity re directly relted to ltertions in the coordintion of the metls in the ctive site of the enzyme. Alkline phosphtse (EC ) is nonspecific phosphomonoesterse found in orgnisms from ll kingdoms of life. The mechnism of the lkline phosphtse rection involves the ttck of serine lkoxide on the phosphorus of the substrte to form trnsient covlent enzymephosphte complex followed by the hydrolysis of the serine phosphte (1). Alignment of the sequences from selection of lkline phosphtses shows tht the enzymes re very well conserved, especilly ner the ctive site. Upon comprison of residues within 10 Å of the phosphte position in the ctive site of the Escherichi coli enzyme to the corresponding residues in other lkline phosphtses, the mjority of enzymes re found to conserve most of these mino cid positions. The residues tht directly interct with the substrte, Ser102 nd Arg166, re conserved in ll cses. In the E. coli enzyme, the ctive site contins two Zn 2+ ions nd one Mg 2+ ion. The residues intercting with the zinc t the M1 1 site (Asp327, His331, nd His412) nd the residues intercting with zinc t the M2 site (Asp51, Asp369, nd His370) re conserved in ll compred sequences. The only This work ws supported in prt by Grnt GM42833 from the Ntionl Institutes of Helth. Dt for this study were mesured t bemlines X12b nd X26c of the Ntionl Synchrotron Light Source. Finncil support comes principlly from the Offices of Biologicl nd Environmentl Reserch nd of Bsic Energy Sciences of the U.S. Deprtment of Energy, nd from the Ntionl Center for Reserch Resources of the Ntionl Institutes of Helth. Coordintes nd observed structure fctor mplitudes for the structures described in this pper hve been deposited in the Protein Dt Bnk (entries 1Y6V nd 1Y7A). * To whom correspondence should be ddressed. E-mil: evn.kntrowitz@bc.edu. Telephone: (617) Fx: (617) vritions occur t mino cids Asp153 nd Lys328 ner the E. coli enzyme Mg 2+ binding site (M3). Invribly, the only chnge observed t E. coli position 153 is from n Asp to His. The most common chnge t E. coli lkline phosphtse position 328 is to Trp, the exception being His found in the Pyrococcus byssi nd eukryotic enzymes. In ddition to lkline phosphtses tht utilize Zn 2+ nd Mg 2+, there re some tht utilize coblt (2, 3). Among the Co 2+ -requiring enzymes, Thermotog mritim lkline phosphtse nd the Bcillus subtilis phoaiii nd phoaiv gene products hve His nd Trp t E. coli positions 153 nd 328, respectively. To test whether positions 153 nd 328 lone or in combintion determine the metl specificity of lkline phosphtse, we previously prepred by site-specific mutgenesis the D153H nd K328W muttions in the E. coli enzyme individully nd in combintion (4). The wild-type nd D153H enzymes showed very little ctivity in the presence of Co 2+. For exmple, when the Zn 2+ nd Mg 2+ re replced with coblt in the wild-type enzyme, the k ct decreses more thn 500-fold (Tble 1). However, the k ct of the coblt-contining K328W enzyme is only 5-1 Abbrevitions: M1, highest-ffinity metl site occupied by Zn 2+ in the wild-type enzyme; M2, second metl site occupied by Zn 2+ in the wild-type enzyme; M3, lowest-ffinity metl site occupied by Mg 2+ in the wild-type enzyme; WT_Zn/Mg, wild-type E. coli lkline phosphtse with Zn 2+ in the M1 nd M2 sites nd Mg 2+ in the M3 site (PDB entry 1ED8); WT_Co, wild-type E. coli lkline phosphtse with Co 2+ in the M1-M3 sites (PDB entry 1Y6V); HW_Co, mutnt version of E. coli lkline phosphtse with Asp153 replced with His nd Lys328 replced with Trp with Co 2+ in the M1-M3 sites (PDB entry 1Y7A); HH_Zn, mutnt version of E. coli lkline phosphtse with Asp153 nd Lys328 re replced with His with Zn 2+ in the M1- M3 sites (PDB entry 1ANI) /bi050155p CCC: $ Americn Chemicl Society Published on Web 05/18/2005

2 Structures of Coblt Alkline Phosphtse Biochemistry, Vol. 44, No. 23, Tble 1: Kinetic Prmeters of the Wild-Type nd Mutnt Alkline Phosphtses under Their Optiml Conditions enzyme k ct (s -1 ) K m (µm) k ct/k m (M -1 s -1 ) metl ph wild type ( ( Zn, Mg 8.0 wild type 0.3 ( ( Co 10.0 D153H 47.4 ( ( Zn, Mg 10.0 K328W ( ( Zn, Mg 10.0 K328W 31.2 ( ( Co, Mg 10.0 D153H/K328W 8.9 ( ( Zn, Mg 10.0 D153H/K328W 43.7 ( ( Co, Mg 10.0 The rections were performed in 1.0 M Tris-HCl t the indicted ph nd 25 C (4). The k ct vlues were clculted from the V mx vlues obtined by using dimer moleculr mss of D. fold lower thn the k ct of this enzyme in the presence of Zn 2+ nd Mg 2+. In the cse of the D153H/K328W enzyme, when the Zn 2+ nd Mg 2+ re replced with coblt, the k ct increses 5-fold (Tble 1) (4). These studies suggested tht the ctive site residues His nd Trp t E. coli enzyme positions 153 nd 328, respectively, prtilly dictte the metl specificity of lkline phosphtse. To understnd the structurl bsis for the ltered metl specificity nd the bility of the D153H/K328W enzyme to utilize coblt for ctlysis, we determined the structures of the inctive wild-type E. coli enzyme with coblt in the ctive site, nd of the ctive D153H/K328W enzyme with coblt in the ctive site. EXPERIMENTAL PROCEDURES Mterils Mgnesium chloride, zinc chloride, sodium chloride, coblt sulfte, sodium dihydrogen phosphte, EDTA, sucrose, nd sodium dodecyl sulfte were purchsed from Sigm Chemicl Co. (St. Louis, MO). Tris nd enzyme grde mmonium sulfte were purchsed from ICN Biomedicls (Cost Mes, CA). Phenyl-Sephrose nd Source 15Q strong nionexchnge resin were purchsed from Amershm Phrmci Biotech (Pisctwy, NJ). Protein Assy Dye nd Chelex 100 resin were obtined from Bio-Rd. Crystl cryomounting loops were purchsed from Hmpton Reserch (Lgun Niguel, CA). Methods Expression nd Purifiction of the Wild-Type nd D153H/ K328W Alkline Phosphtses. The wild-type nd mutnt enzymes were isolted from the pproprite pek548/sm547 plsmid/strin combintions (4) by the method described previously (5). An dditionl phenyl-sephrose column purifiction step ws used for the D153H/K328W enzyme (4). The purities of the enzymes were checked by SDSpolycrylmide gel electrophoresis (6). The Bio-Rd version of Brdford s dye-binding ssy ws used for determintion of protein concentrtions using the wild-type enzyme s the stndrd (7). Both wild-type nd D153H/K328W enzymes were concentrted to pproximtely 20 mg/ml before use. Preprtion of Wild-Type nd Double Mutnt Enzymes with Coblt. The wild-type nd D153H/K328W lkline phosphtses were rendered metl-free using procedure dpted from Dirnbch et l. (8). Five milliliter of 20 mg/ ml enzyme ws dilyzed ginst 50 mm Tris nd 10 mm EDTA (ph 8.0) to remove extrneous metls nd phosphte. Then the enzyme solution ws dilyzed twice versus 40% mmonium sulfte nd 10 mm EDTA (ph 9.5), followed by extensive dilysis versus 10 mm Tris nd 10 mm EDTA (ph 9.0) to remove the mmonium sulfte. The ph ws redjusted by nother dilysis in 100 mm Tris nd 10 mm EDTA (ph 8.0). Finlly, the enzyme solution ws dilyzed ginst 100 mm Tris nd Chelex (2.5 g/l) (ph 8.0) to remove the EDTA. The enzyme solutions were filtered, nd the ctivity ws determined. The lck of enzymtic ctivity confirmed the bsence of metls in the ctive site (4). Coblt sulfte ws then dded to the poenzyme solution to finl concentrtion of 10 mm. Crystlliztion. The wild-type nd D153H/K328W coblt enzymes were dilyzed versus zinc- nd mgnesium-free 10 mm coblt sulfte, 100 mm Tris, 0.85 M (NH 4 ) 2 SO 4,2 mm NH 2 PO 4 (ph 9.5) protein-stbiliztion buffer, before being concentrted to 40 mg/ml. Vpor diffusion ws used to crystllize ech enzyme using 2 µl hnging drops. Within pproximtely 1 week, crystls of the WT_Co enzyme formed in reservoirs with mmonium sulfte concentrtions rnging from 2.0 to 2.2 M. Crystl sizes vried from 0.6 mm 0.3 mm 0.3 mm to 0.8 mm 0.6 mm 0.3 mm. Crystls of the HW_Co enzyme required 3 months to form, in reservoirs with the mmonium sulfte concentrtion rnging from 2.2 to 2.3 M. The size of the crystls formed vried from 0.8 mm 0.3 mm 0.3 mm to 2.2 mm 0.6 mm 0.3 mm. Dt Collection. Before being mounted, the crystls were trnsferred into crystl stbiliztion buffer composed of 3.0 M (NH 4 ) 2 SO 4, 100 mm Tris, 2 mm NH 2 PO 4, nd 10 mm CoSO 4 (ph 7.5) for t lest 24 h. Crystls were trnsferred to cryo-loops nd soked in mixture of 80% crystl stbiliztion buffer nd 20% glycerol for 1 min before being dipped in liquid nitrogen. Dt were collected t the Ntionl Synchrotron Light Source t Brookhven Ntionl Lbortory (Upton, NY) on bemlines X12b nd X26c. Diffrction dt were collected to 1.60 nd 1.77 Å for the WT_Co nd HW_Co crystls, respectively (Tble 2). The dt sets were processed with HKL2000 (9). Model Building nd Structure Refinement. The initil model for the refinement of the WT_Co nd HW_Co structures ws bsed on the coordintes of E. coli lkline phosphtse determined to 1.75 Å resolution with ll lignds removed from the ctive sites (PDB entry 1ED8) (10). Although the crystls of WT_Co nd HW_Co re in the sme spce group s those of the strting model, there were significnt differences (>3 Å) long the b nd c xes. R nd R free equled 28 nd 30%, respectively, fter the first rigid body nd simulted nneling refinement in CNS (11). To improve the initil model, utomted moleculr replcement (AMoRe) ws performed on both dt sets using monomer s the strting model to improve the dimer interfce nd crystl lttice pcking. After model building with AMoRe hd been crried out, round of refinement ws performed with CNS. Ten percent of the reflections were not used in the refinement nd were used to clculte R free. The metls, phosphte, nd sulfte were introduced into both structures. After ech refinement cycle, visul inspection nd mnul rebuilding were performed in XtlView (12) to improve the working R nd R free vlues. The finl stges of the refinement were performed using SHELX-97 (13). After the first round of refinement

3 8380 Biochemistry, Vol. 44, No. 23, 2005 Wng et l. Tble 2: Dt Collection nd Refinement Summry of the WT_Co nd HW_Co Structures WT_Co HW_Co dt collection spce group I222 I222 resolution (Å) ( ) ( ) totl no. of reflections no. of unique reflections redundncy 6.9 (6.5) 12.0 (10.3) completeness (%) (89.6) unit cell (Å) ) ) b ) b ) c ) c ) ngles (deg) R)β ) γ ) 90 R)β ) γ ) 90 R merge (%),b 5.3 (28.8) 8.5 (23.9) refinement resolution (Å) verge I/σ R R free no. of wters verge B fctor (Å 2 ) rms devitions bonds (Å) ngles (deg) dihedrls (deg) Dt in prentheses correspond to the highest-resolution shell. b R merge ) (I hkl - I hkl )/ I hkl, where I hkl is the observed intensity nd I hkl is the men intensity of the observed intensity. in SHELX-97, wters were dded. The models were returned to CNS for finl B fctor refinement. The mobility of ctive site metls nd phosphte ws evluted by inspecting the F o - F c electron density mp for lternte positions nd by occupncy refinement in CNS. The finl R nd R free vlues s well s the refinement sttistics re reported in Tble 2. RESULTS Structures of the Wild-Type nd D153H/K328W Coblt Enzymes. The dt for wild-type AP with coblt (WT_Co) nd the D153H/K328W enzyme with coblt (HW_Co) were integrted, scled, nd verged to spce group I222, the sme spce group tht ws observed for the wild-type structure with zinc nd mgnesium (WT_Zn/Mg) (PDB entry 1ED8) (10). The WT_Co nd HW_Co structures were refined to R vlues of 19.1 nd 20.5% nd R free vlues of 21.2 nd 23.8% t resolutions of 1.60 nd 1.77 Å, respectively. The unit cell dimensions, dt collection sttistics, nd refinement sttistics re given in Tble 2. The electron density in the ctive site region of the WT_Co structure is shown in Figure 1A. When the 2F o - F c electron density mp is contoured t 2.0σ or lower, electron density completely covers every residue in the ctive site, indicting the ctive site is well-refined. The position of the side chin of Lys328 is stbilized by interctions with Asp327 nd Asp153. Lys328 forms wter-medited interction with Asp327 nd slt link with Asp153. There is lso wtermedited interction between Asp153 nd Arg166. Inorgnic phosphte (P i ), the product of the rection, is positioned in the ctive site pocket vi three coordintion bonds to the coblt ions in the M1 nd M2 sites. Two phosphte oxygens lso interct in bidentte fshion with the terminl nitrogens of Arg166. The verge B fctor for the side chin of Arg166 is Å 2, nd the B fctor for the P i is Å 2 t 100% occupncy (Tble 3). The electron density in the ctive site of the HW_Co structure is shown in Figure 1B. The positions of the two mutnt residues, His153 nd Trp328, were confirmed by evlution of simulted nneling omit mps produced with CNS (11). Trp328 is repositioned towrd the solvent nd wy from the ctive site. His153 coordintes directly to the coblt ion in the M3 site. The B fctors for the Trp328 nd His153 side chins were nd Å 2, respectively. The coordintion of His153 to the coblt ion prevents His153 from forming wter-medited interction with Arg166, which does occur in the wild-type structure. In this structure, Arg166 intercts in bidendte fshion with wter molecule nd is involved in binding P i. The verge B fctor of the Arg166 side chin is Å 2, while the verge B fctor for the P i is Å 2 with n occupncy of 60% (Tble 3). Geometry of the Three Metls in the ActiVe Site of the WT_Co Structure. In the WT_Co structure, ech ctive site hs three coblt ions bound in positions very similr to those observed for the zinc nd mgnesium ions in the WT_Zn/ Mg structure. A summry of the interctions involving the three coblt ions in the WT_Co structure s well s the corresponding distnces nd ngles cn be found in Tbles 4 nd 5, respectively. The coblt in the M1 site is coordinted to Asp327, His331, His412, nd P i, nd dopts pproximte octhedrl geometry (see Figure 2). His412 NE2, Asp327 OD1, Asp327 OD2, nd P i O2 re coplnr, ech intercting with the coblt t distnces between 2.02 nd 2.42 Å. These interctions re confirmed by the presence of electron density t 2.0σ (see Figure 2 nd Tble 4). The ngles between the two bonding toms nd the coblt re ll close to 90 except in the cse of the Asp327 OD1 -Co-Asp327 OD2 ngle, which is 57.8 due to the restrints imposed by the crboxyl group of Asp327 (Tble 5). The requirement to keep the two oxygen toms of Asp327 close together prevents these oxygen toms from forming optiml coordintion with the coblt. The picl His331 NE2 -Co-picl PO 4 O3 ngle of 169.4, which is close to 180, lso supports n octhedrl geometry for the coblt t the M1 site. The coblt ion in the M2 site dopts trigonl bipyrmidl geometry (see Figure 2). Ser102 OG, His370 NE2, Asp369 OD1, nd the coblt re in the sme plne, nd the ngles between the two bonding toms nd the coblt in the equtoril plne re 131.5, 113.5, nd 115.1, ll resonbly close to the expected vlue of 120. The picl P i O3 -Co-picl Asp369 OD1 ngle of devites slightly from the idel vlue of 180. However, this distortion my be due to the bckbone restrints the enzyme imposes upon residues in the ctive site. The coblt ion in the M3 site lso dopts n octhedrl geometry. Three wter lignds to the coblt offer lower constrints, mking it much esier for this coblt to ttin perfect octhedrl geometry. The coordinte bond distnces rnge from 1.91 to 2.15 Å, nd the ngles between these bonds rnge from 83.3 to 98.1, ll flling within the idel coordintion bond distnce or ngle rnge (see Figure 2). Geometry of the Three Metls in the ActiVe Site of the HW_Co Structure. The geometries of coblt t the M1 nd M2 sites in the HW_Co structure re the sme s those in the WT_Co structure: octhedrl nd trigonl bipyrmidl, bsed on the observed bond distnces nd ngles (see Figure 2).

4 Structures of Coblt Alkline Phosphtse Biochemistry, Vol. 44, No. 23, FIGURE 1: Stereoview of the ctive site of the WT_Co nd HW_Co structures. Shown re the 2F o - F c electron density mps for (A) WT_Co (2.0σ) nd (B) HW_Co (1.2σ, to show the density of the Arg166 nd the P i ). Overlid on the electron density re the finl refined coordintes. Wter molecules re shown s red spheres nd Co toms s lrger cyn spheres. Dshed lines represent hydrogen bonds. Figures 1-5 were prepred using MOLSCRIPT (24). Tble 3: Occupncy nd B Fctors of Some Lignds nd Active Site Residues in the WT_Zn/Mg, WT_Co, HH_Zn, nd HW_Co Structures B fctor (Å 2 ) residue WT_Zn/Mg WT_Co HH_Zn HW_Co Ser Arg Asp/His Lys/His/Trp P b i 1.00/ / / /70.84 The vlues reported re the verge B fctors of the side chins of the A nd B chins. b Reported re the occupncy nd B fctor of the P i verged over the A nd B chins. For the coblt in the M3 site, the side chin of His153 becomes direct lignd nd replces two of the wter molecules tht coordinte to the M3 coblt in the WT_Co structure. Asp51 OD1, Glu322 OE2, His153 ND1, nd this coblt re lmost coplnr, with equtoril ngles rnging from to (Tble 4). In ddition, the Glu322 OE2 -Co- Asp51 OD1 ngle is shifted from 98.1 in the WT_Co structure to in HW_Co structure. Tke together, these observed ngles suggest tht the geometry of coblt t the M3 site hs chnged from octhedrl in the WT_Co structure to trigonl bipyrmidl in the HW_Co structure (see Figure 2). ActiVe Site Comprison of the WT_Co nd WT_Zn/Mg Structures. Comprison of the WT_Co nd WT_Zn/Mg structures fter lest-squres fit of the coordintes reveled two mjor differences between the structures in the ctive site region. First, there is n ltertion in the position of the Ser102 side chin nd, second, chnge in the position of the P i. In the WT_Co structure, there is only one conformtion for the side chin of Ser102, in which Ser102 OG forms very strong coordinte bond with the M2 coblt. In contrst, there re two conformtions of the side chin of Ser102 with occupncies of pproximtely 40 nd 60% in the WT_Zn/ Mg structure (PDB entry 1ED8): the predominnt conformtion hs the hydroxyl of Ser102 coordinted to zinc, wheres in the lterntive conformtion, this hydroxyl forms hydrogen bond with Thr155 (see Figure 3). In the WT_Co structure, the interction between Ser102 OG nd the M2 coblt is very strong, s judged by the persistence of the electron density to 4.0σ. This strong coordinte bond would prevent the hydroxyl group from rotting to ttck the substrte, which is consistent with the observed decresed k ct vlue of the WT_Co enzyme compred with tht of the the WT_Zn/Mg enzyme (4). The second mjor difference between the WT_Co nd WT_Zn/Mg structures is the precise coordintion of the P i. In the WT_Co structure, the P i is shifted 0.16 Å closer to the M1 coblt nd rotted 23 so tht the distnce between P O3 i nd this coblt decreses from 2.87 to 2.34 Å, llowing direct coordintion with the coblt. The three coordinte interctions between the P i nd the coblt t the M1 nd M2

5 8382 Biochemistry, Vol. 44, No. 23, 2005 Wng et l. Tble 4: Metl-Lignd Distnces in the Wild Type with Zinc, the Wild Type with Coblt, D153H/K328H with Zinc, nd D153H/K328W with Coblt distnce (Å) WT_Zn/Mg b WT_Co b,c HH_Zn b HW_Co b,c Zn1/Co1 His412 NE His331 NE Asp327 OD Asp327 OD PO 4 O PO 4 O Zn2/Co2 Ser102 OG Asp51 OD Asp369 OD His370 NE PO 4 O Zn3(Mg3)/Co3 Asp51 OD Glu322 OE Thr155 OG Asp/His153 OD1/NE H 2O H 2O H 2O The number fter the metl refers to the prticulr metl site in the enzyme (e.g., M1, M2, or M3). b WT_Zn/Mg, wild-type with zinc nd mgnesium (PDB entry 1ED8); HH_Zn, D153H/K328H with zinc (PDB entry 1ANI); WT_Co: wild type with coblt; HW_Co, D153H/K328W with coblt. c The distnces re the verge of the distnces in A nd B chins. Tble 5: Lignd-Metl-Lignd Angles in the WT_Co nd HW_Co Structures ngle (deg) WT_Co HW_Co Co1 b His331 NE2 O3 -Co-PO His412 NE2 O2 -Co-PO Asp327 OD2 O2 -Co-PO Asp327 OD2 -Co-Asp327 OD His412 NE2 -Co-Asp327 OD Co2 b Asp369 OD1 O3 -Co-PO Asp51 OD2 -Co-His370 NE Ser102 OG -Co-His370 NE Asp51 OD2 -Co-Ser102 OG Co3 b Thr155 OG1 -Co-H 2O Glu322 OE2 -Co-Asp51 OD Asp51 OD1 -Co-H 2O 92.4 Asp322 OE2 -Co-H 2O 86.4 H 2O-Co-H 2O 83.3 Glu322 OE2 -Co-His153 NE Asp51 OD1 -Co-His153 NE The vlues cme from the verge of the A chin ngles nd B chin ngles. b The number fter the metl refers to the prticulr metl site in the enzyme (e.g., M1, M2, or M3). sites suggest tht the P i is more tightly bound in the ctive site of the WT_Co structure thn in the WT_Zn/Mg structure. Comprison of the ActiVe Sites of the WT_Co nd HW_Co Structures. Anlysis of 2F o - F c, F o - F c, nd simulted nneling omit mps indicted tht the HW_Co structure differed significntly from the WT_Co structure loclly in the ctive site region (see Figure 4). The slt link between Asp153 nd Lys328, present in the WT_Zn/Mg nd WT_Co structures, is bsent in the HW_Co structure. In the HW_Co structure, Trp328 is found flipped out of the ctive site; furthermore, the new position is not well defined, s indicted by lck of electron density even t contour level s low s 1.0σ. The side chin of Trp328 hs n verge B fctor of Å 2. The side chin of His153 coordintes directly with the M3 coblt, chnging the coblt geometry from octhedrl in the WT_Co structure to trigonl bipyrmidl in the HW_Co structure. P i is loosely bound in the ctive site pocket of the HW_Co structure, exhibiting n occupncy of 0.60 with B fctor of Å 2. These vlues provide n explntion for the reduced ffinity of the substrte observed for the HW_Co enzyme s compred to those for the WT_Co nd WT_Zn/ Mg enzymes (4). Structurl Comprison of the ActiVe Site of the HW_Co nd HH_Zn Structures. In the structure of the D153H/K328H lkline phosphtse (HH_Zn, PDB entry 1ANI) (14), ll the metl sites hve zinc present even though the crystl stbiliztion buffer contined both Zn 2+ nd Mg 2+. The D153H muttion resulted in the conversion of the M3 site for mgnesium to zinc site, s ws verified in the structure of the D153H single mutnt (PDB entry 2ANH) (14). When the HW_Co nd HH_Zn structures were compred fter superposition, differences in the position of the P i nd the side chins of some ctive site residues were observed, s well s the coordintion geometry of the metl ions (see Figure 5). In contrst to its loction in the HW_Co structure, in the HH_Zn structure the P i no longer coordinted to the M1 nd M2 metls nd hs moved 3.0 Å out of the ctive site towrd the solvent. Arg166 is repositioned, losing two coordinte bonds with wter molecules, nd shows two wek hydrogen bonds to the P i, indicted by longer hydrogen bond lengths of 3.4 nd 2.9 Å. All three zinc ions dopt tetrhedrl or distorted tetrhedrl geometry bsed on the metl-lignd distnces in the HH_Zn structure (Tble 3). In the HW_Co structure, wter molecule coordintes to the M3 coblt; however, there is no wter coordinted to the zinc t the M3 site in the HH_Zn structure. This wter molecule switches the geometry of the metl from tetrhedrl in the HH_Zn structure to trigonl bipyrmidl in the HW_Co structure. DISCUSSION The metl specificity of number of lkline phosphtses is known. Mny require zinc nd mgnesium; however, some

6 Structures of Coblt Alkline Phosphtse Biochemistry, Vol. 44, No. 23, FIGURE 2: Metl geometry of the six coblt ions in the WT_Co (top) nd HW_Co (bottom) structures. Shown re the 2F o - F c electron density mps contoured t 2.0σ for the WT_Co structure, 1.2σ for the M1 nd M2 sites, nd 1.5σ for the M3 site for the HW_Co structure. Overlid on the electron density re the finl refined coordintes. FIGURE 3: Comprison of the position of Ser102 nd P i in the WT_Co nd WT_Zn/Mg structures. Shown is the 2F o - F c electron density mp of the WT_Co structure (2.0σ). Overlid on the electron density re the finl refined coordintes of the WT_Co structure (elementl colors, thick lines) nd the WT_Zn/Mg structure (10) (mgent, thin lines). The lignds with unchnged positions re not shown. In the WT_Co structure, the P i hs three coordinte bonds with coblt in the M1 nd M2 sites, while the Ser102 hydroxyl group coordintes with coblt in the M2 site. In the WT_Zn/Mg structure, P i hs one coordinte bond to the M1 nd M2 zinc ions, while the Ser102 hydroxyl group exhibits two conformtions, one coordinted to the zinc ion in the M2 site nd the other intercting with wter (hydroxyl) lignd to the Mg 2+ in the M3 site. require coblt (2, 3). A comprison of metl specificities nd sequence lignments revels tht enzymes tht require zinc nd mgnesium hve Asp t position 153 nd Lys t position 328 (E. coli numbering), while those tht require coblt hve His t position 153 nd Trp t position 328. We hve previously mutted E. coli AP, introducing His nd Trp t positions 153 nd 328, respectively (4). The D153H/K328W coblt enzyme hs k ct 145-fold higher thn tht of the coblt-contining wild-type enzyme. Furthermore, the k ct of the D153H/K328W coblt enzyme is only 3-fold lower thn the k ct of the Zn- nd Mg-contining wild-type enzyme (see Tble 1). Here we use X-ry crystllogrphy to determine the structures of the wild-type nd D153H/K328W enzymes with coblt s the metl cofctor to clrify the structurl bsis of the ltered metl specificity of these lkline phosphtses. One of the mjor differences between zinc nd coblt is tht the 3d orbitl is filled for zinc (3d 10 ) nd only prtilly filled for coblt (3d 7 ). This d orbitl difference llows coblt to form low-spin complexes, while zinc cn form only highspin complexes. Zn(II) is zinc s predominte oxidtion stte, nd it cn form high-spin complexes with tetrhedrl, trigonl bipyrmidl, or octhedrl geometries. Co(II) nd Co(III) re the predominte oxidtion sttes of coblt, llowing the formtion of high-spin or low-spin complexes. Co(II) cn form low-spin trigonl bipyrmidl s well s high-spin octhedrl geometry, while Co(III) predomintely forms lowspin octhedrl complexes (15). M1 Metl Binding Site. The M1 site in the WT_Zn/Mg enzyme contins zinc nd hs tetrgonl pyrmidl geometry (16). Zn 2+ intercts with His331 NE2, His412 NE2, Asp327 OD1, Asp327 OD2, nd one oxygen of the P i. In both the WT_Co nd HW_Co structures, the coblt t the M1

7 8384 Biochemistry, Vol. 44, No. 23, 2005 Wng et l. FIGURE 4: Comprison of the coordintion of coblt, wter, nd P i in the ctive sites of the HW_Co (elementl colors, thick lines) nd WT_Co (mgent, thin lines) structures. Shown is the 2F o - F c electron density mp of the WT_Co structure (1.2σ). Wter molecules re represented s red spheres nd coblt toms s cyn spheres. The side chins with unchnged positions re not shown. FIGURE 5: Comprison of the ctive sites of the HW_Co (elementl colors, thick lines) nd HH_Zn (14) (mgent, thin) structures. Metl positions re represented s cyn spheres, nd the wter molecule is represented s red sphere. Dshed lines represent hydrogen bonding interctions. site hs octhedrl geometry (see Figure 2). This is consistent with the fct tht in known structures of coblt-contining proteins, the coblt lwys dopts octhedrl or trigonl bipyrmidl geometry independent of the oxidtion stte (17-19). The interctions between the coblt nd its lignds re very strong, bsed upon the observed electron density contour levels in the 2F o - F c electron density mps. These strong interctions re consistent with low-spin Co(III), but the bond lengths re similr to tht observed in the WT_Zn/ Mg enzyme, suggesting high-spin Co(II). M2 Metl Binding Site. The M2 site in the WT_Zn/Mg enzyme contins zinc nd hs distorted tetrhedrl geometry. Zn 2+ intercts with His370 NE2, Asp51 OD1, Asp369 OD1, nd one oxygen of P i (16). In contrst to the WT_Zn/Mg structure, the coblt t the M2 site is observed to hve trigonl bipyrmidl geometry in both the WT_Co nd HW_Co structures (see Figure 2). M3 Metl Site. The M3 site in the WT_Zn/Mg enzyme contins mgnesium nd hs octhedrl geometry. The Mg 2+ is coordinted to three oxygen toms from Asp51 OD2, Glu322 OE2, nd Thr155 OG1 nd three oxygen toms from wter molecules (16). Two of these wters re held in plce by dditionl hydrogen bonding interctions with the crboxylte of Asp153. In ddition, the crboxylte of Asp51 cts s bridge between the M2 nd M3 sites. In the WT_Co structure, the geometry of the coblt t the M3 site is similr to tht of Mg in the WT_Zn/Mg structure. However, in the HW_Co structure, the coordintion t this site chnges from octhedrl to trigonl bipyrmidl (see Figure 2). In the WT_Co structure, there is sufficient spce for three wter molecules to pproch the coblt, llowing the coblt to dopt octhedrl geometry. In contrst, in the HW_Co structure, His153 NE2 forms coordinte bond to the coblt, tking the spce of two of the three wter molecules tht interct with the Mg 2+ in the WT_Zn/Mg structure (see Figure 4). The loss of one coordinting lignd mkes it energeticlly unfvorble for the coblt to mintin octhedrl geometry, so it dopts dsp 3 hybridiztion nd trigonl bipyrmidl geometry. The trigonl bipyrmidl geometry is verified by the expnsion of the Glu322 OE2 -Co-Asp51 OD1 ngle from 98.1 to 110.4, nd the other two equtoril ngles of nd (Tble 4). Co 2+ Versus Zn 2+. In the HH_Zn structure, ll three metl sites re occupied by zinc (14). The zinc t the M3 site dopts tetrhedrl geometry with Asp51 OD2, Thr155 OG1, Glu322 OE2, nd His153 NE2 s lignds. In the HW_Co structure, the coblt t the M3 site dopts trigonl bipyrmidl geometry. This observtion is consistent with the fct tht zinc prefers tetrhedrl over trigonl bipyrmidl geometry. WT_Co Versus WT_Zn/Mg Structures. Although the metl present in the three metl binding sites is the only difference between the WT_Co nd WT_Zn/Mg enzymes, these two enzymes exhibit entirely different ctlytic ctivities. The wild-type enzyme in the presence of Zn 2+ nd Mg 2+ hs 5000-fold higher ctlytic efficiency thn the wild-type enzyme in the presence of coblt t bsic ph (see Tble 1) (4). The coblt ions in the ctive site coordinte with P i s well s with Ser102 OG to stisfy their tendency to form n octhedrl/trigonl bipyrmidl geometry. For the wild-type enzyme with zinc nd mgnesium, it is known tht the relese

8 Structures of Coblt Alkline Phosphtse Biochemistry, Vol. 44, No. 23, of the P i from the noncovlent E P i complex is the rtedetermining step t bsic ph (20, 21). In the cse of the WT_Co enzyme, the three coordintion bonds between the coblt nd P i enhnce phosphte ffinity, impeding the rtedetermining step (see Figure 3). Additionl rte reduction cn lso be explined by the strong coordintion between the coblt t the M2 site nd Ser102 OG, which would retrd the ttck of the serine hydroxyl on the phosphorus of the substrte. The HW_Co Enzyme Hs Higher ActiVity thn the WT_Co Enzyme. For the wild-type enzyme, it is proposed tht Asp153 helps position the side chin of Arg166, by wter-medited interction, to bind P i (22). Since this interction is bsent in the HW_Co structure (see Figure 4), these muttions should increse the flexibility of the Arg166 side chin, which in turn should result in reduced P i ffinity. Higher B fctors determined for Arg166 in the HW_Co structure support the notion tht this side chin hs enhnced flexibility, nd help explin why the HW_Co enzyme hd 20-fold higher ctlytic efficiency thn the WT_Co enzyme (4). D153H/K328W Alkline Phosphtse Prefers Coblt for ActiVity. Previous kinetic studies hve shown tht the wildtype enzyme loses lmost ll ctlytic ctivity when the zinc nd mgnesium in the ctive site re chnged to coblt. However, only two muttions (D153H nd K328W) re required to convert the wild-type enzyme into n enzyme tht cn function effectively with coblt (4) (see Tble 1). Our studies provide structurl explntion for why the wildtype enzyme exhibits lmost no ctivity when coblt is the metl cofctor, wheres the HW_Co enzyme is ctive with coblt s the metl cofctor. Stble complexes of coblt re low-spin with stronger coordintion bonds thn those in the high-spin complexes formed by zinc ions. These strong interctions hold ctive site residues tightly nd therefore my severely compromise the bility of the Ser102 hydroxyl to function s nucleophile. The strong interction between Ser102 OG nd the coblt explins the diminished ctivity in the WT_Co enzyme compred to tht in the WT_Zn/Mg enzyme. Summry. The tighter binding of the P i s well s the rigid position of Ser102 OG in the WT_Co structure cuses slower rte of P i relese, s well s reduction in the rte of the nucleophilic ttck by Ser102 OG on the substrte. These chnges explin the drmtic decrese in enzymtic ctivity when zinc nd mgnesium in the wild-type enzyme re replced with coblt. A comprison of the WT_Co with HW_Co structures clrifies the influence of the muttion on metl ion specificity. When Asp153 is mutted to His, His153 directly coordintes to the coblt in the M3 site, cusing switch of geometry from octhedrl in the WT_Co structure to trigonl bipyrmidl in the HW_Co structure. Becuse the crboxylte of Asp51 bridges the M2 nd M3 sites, this ltertion in coordinte geometry t the M3 site hs ripple effect, resulting in weker interction between Ser102 OG nd the coblt t the M2 site s well s weker interction between P i nd the coblt. Tken together, these ltertions result in substntilly higher enzymtic ctivity in the HW_Co enzyme compred to tht in the WT_Co enzyme. Finlly, the comprison of HW_Co nd HH_Zn structures provides structurl detils bout how different metl ions influence ctive site coordintion. The requirement of t lest five coordintion sites by coblt lters the geometry of the M3 site from tetrhedrl in the HH_Zn structure to trigonl bipyrmidl in the HW_Co structure. This ltertion in M3 geometry results in substntilly higher ctlytic ctivity for the HH_Zn enzyme s compred to tht of the wild-type enzyme (23). Overll, these results provide structurl bsis for understnding how metl substitutions in the ctive site of lkline phosphtse influence the ctlytic ctivity. 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