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Copyright © 2007 by The National Academy of Sciences of the USA Biochemistry Chymotryptic specificity determinants in the 1.0 Å structure of the zinc-inhibited human tissue kallikrein 7 †Max-Planck-Institut für Biochemie, Proteinase Research Group, Am Klopferspitz 18, 82152 Martinsried, Germany; ‡Max-Planck-Institut für Biochemie, Strukturforschung, Am Klopferspitz 18, 82152 Martinsried, Germany; §Klinische Forschergruppe der Frauenklinik der TU München, Ismaninger Strasse 22, 81675 Munich, Germany; ¶Department of Dermatology, University of Pennsylvania, 415 Curie Boulevard, Philadelphia, PA 19104; and ‖School of Biosciences, Cardiff University, Cardiff CF10 3TL, United Kingdom ††To whom correspondence may be addressed. E-mail: huber/at/biochem.mpg.de or Email: goettig/at/biochem.mpg.de Contributed by Robert Huber, August 18, 2007 .Author contributions: V.M., N.M.S., R.H., W.B., and P.G. designed research; M.D., P.H., N.M.S., T.S., and P.G. performed research; M.D., P.H., N.M.S., and P.G. analyzed data; and M.D., V.M., W.B., and P.G. wrote the paper. Received July 27, 2007. Abstract hK7 or human stratum corneum chymotryptic enzyme belongs to the human tissue kallikrein (hKs) serine proteinase family and is strongly expressed in the upper layers of the epidermis. It participates in skin desquamation but is also implicated in diverse skin diseases and is a potential biomarker of ovarian cancer. We have solved x-ray structures of recombinant active hK7 at medium and atomic resolution in the presence of the inhibitors succinyl-Ala-Ala-Pro-Phe-chloromethyl ketone and Ala-Ala-Phe-chloromethyl ketone. The most distinguishing features of hK7 are the short 70–80 loop and the unique S1 pocket, which prefers P1 Tyr residues, as shown by kinetic data. Similar to several other kallikreins, the enzyme activity is inhibited by Zn2+ and Cu2+ at low micromolar concentrations. Biochemical analyses of the mutants H99A and H41F confirm that only the metal-binding site at His99 close to the catalytic triad accounts for the noncompetitive Zn2+ inhibition type. Additionally, hK7 exhibits large positively charged surface patches, representing putative exosites for prime side substrate recognition. Keywords: 99 loop, desquamation, metal-binding proteinase, Netherlon syndrome Human tissue kallikrein 7 (hK7), also called KLK7 or stratum corneum chymotryptic enzyme, is a member of the new human tissue kallikreins that lack the “kallikrein” insert of the 99 loop present in hK1–hK3. It is highly expressed in the upper spinous and granular layers of the epidermis (1) and was initially purified from human stratum corneum, the outermost layer of skin (2), where it plays a significant role in physiological and pathophysiological processes of the skin (3). hK7 is biosynthesized as an inactive precursor with a 22-aa signal peptide, followed by a 7-aa activation peptide and a 226-aa catalytic domain. After cleavage of the signal peptide, the proenzyme is activated in vivo by a still unknown extracellular protease with tryptic specificity, whereas in vitro hK5 or stratum corneum trypsin-like serine protease is able to activate pro-hK7 (4). The colocalization of hK5 and hK7 in human skin suggests a functional relationship (5, 6). Because hK7 had been first identified in the skin, later studies focused mainly on its (patho-)physiological function in the epidermis. It was uncovered that hK7 and hK5 degrade intercellular cohesive structures in the stratum corneum, the so-called corneodesmosomes, a process that is required for shedding of cells at the skin surface, a prerequisite for the continuous regeneration of the skin (2–4, 7). Several protein components of the corneodesmosomes, such as desmoglein1, desmocollin1, and corneodesmosin, are good in vitro substrates of both hK7 and hK5 (4). However, an elevated expression of hK7 in the epidermis leads to increased proteolytic activity, pathological desquamation, and inflammation in severe skin diseases such as Netherton syndrome, psoriasis, and atopic dermatitis (5, 7–10). Additionally, hK5 and hK7 exhibit several proinflammatory effects, including the activation of certain cytokines, the attraction of leukocytes, and the induction of proinflammatory activation cascades such as the kallikrein/kinin and complement systems (11). Furthermore, hK7 may participate in multiple processes leading to invasive and metastatic tumor growth, especially in ovarian cancer. Whereas in healthy ovarian tissue, hK7 is produced at moderate concentrations, high levels of hK7 mRNA or protein were identified in ovarian cancers (11–15). The up to 15-fold hK7 overproduction correlates with ovarian cancer stage (16), and, moreover, a high level of hK7 mRNA is associated with a reduced overall survival of ovarian cancer patients (17). In line with these observations, overexpression of the KLK4, 5, 6, and 7 genes in a mouse tumor model increased the malignant phenotype of ovarian cancer cells (18). Thus, hK7 may contribute to metastasis by degrading extracellular matrix and adhesion molecules, enabling the tumor cells to disseminate from the primary tumor. hK7 is one of the few human tissue kallikreins with well defined physiological and pathophysiological functions, and the first example of this family with chymotrypsin-like specificity to be crystallized as recombinant protein that we have purified from insect cells (hK7I) and from Escherichia coli (hK7E). The combined analysis of the hK7 structure and its substrate preference, which we have investigated in a specificity-profiling study (19), provides insights into the molecular determinants of the unique enzyme specificity and metal ion regulation. Results and Discussion Enzymatic Activity and Inhibition of hK7. Parameters of enzyme kinetics for recombinant hK7E were determined with fluorogenic substrates containing a single amino acid, to assess the distinct specificity of the S1 pocket. Both substrates exhibited a slow turnover at 25°C: for Phe-7-amino-4-methylcoumarin (Phe-AMC), values of Km = 44.3 μM, kcat = 0.000016 s−1, and kcat/Km = 0.36 M−1 s−1 were obtained; and for Tyr-AMC, values of Km = 40.2 μM, kcat = 0.000033 s−1, and kcat/Km = 0.82 M−1 s−1 were found. Thus, hK7 cleaves substrates with Tyr at P1 significantly faster, mainly because of an increased kcat value. Even for the tetrapeptidic substrate succinyl (Suc)-Ala-Val-Pro-Phe(AVPF)-pNA a kcat/Km of only 16.0 M−1 s−1 has been reported, indicating the requirement of extended substrate recognition for more efficient catalysis (20). Zinc and copper ions have a strong inhibitory effect on the hydrolytic activity of hK7, whereas calcium ions cause only a slight enhancement of the activity. For Zn2+, an inhibition constant Ki(app) of 10 μM was obtained with the substrate Suc-Ala-Ala-Pro-Phe(AAPF)-AMC, and, similarly, Cu2+ inhibited the enzymatic activity of hK7 at 0.6 μM (Fig. 1
Overall Structure. Four hK7 crystal structures of identical polypeptide length containing two different peptidic inhibitors were solved. The hK7I structure in complex with a covalently bound Suc-AAPF-chloromethyl ketone (CMK) inhibitor was determined to 2.0 Å and 1.0 Å resolution, respectively. Also, a structure of this inhibitor complex with copper ions was solved at 2.1 Å. In contrast, refolded hK7E contains the covalently linked AAF-CMK and was refined to 2.6 Å (Table 1). These structures are rather similar, as reflected by the 0.4 Å rmsd of the Cα carbons, whereas significant deviations of the main chain only occurred in the surface loops between residues 36 and 38, and 70 and 80, according to the chymotrypsinogen numbering for tissue kallikreins (22), indicating an increased flexibility.
The hK7 molecule resembles an oblate ellipsoid with diameters of 35 and 50 Å (Fig. 2
In mature hK7, the polypeptide chain starts with Ile16, which forms via its α-ammonium group an internal salt bridge with the side-chain carboxylate of Asp194. Formation of this salt bridge induces a functional active site as it stabilizes the oxyanion hole and a correctly shaped S1 pocket, which is accompanied by a rigidification of the activation domain (23, 24) (Fig. 2 Of particular interest are two large positively charged surface patches of hK7, which are reminiscent of the functionally important anion-binding exosites of thrombin (26) (Fig. 2 Active-Site Cleft and Specificity. The residues of the catalytic triad, Ser195, His57, Asp102, and the oxyanion hole, constituted by the main-chain amide nitrogens of Gly193 and Ser195, are arranged in the active-site cleft of hK7 as in chymotrypsin (Fig. 2
Both peptidic chloromethyl ketone inhibitors bind to the active-site cleft of hK7 in a canonical manner (Figs. 2 Details of the High-Resolution Structure. Although the 37 and 70–80 loops exhibit some disorder at 1.0 Å resolution, as seen in alternate atom positions both in the main chain (Leu74, A74A) and several side chains, the relatively short kallikrein/99 loop seems to be quite rigid. The α-ammonium group of Ile16 is tightly bound by the carboxylate of Asp194 and the carbonyl O of Thr143, whereas the following residues are more flexible, in particular, the main-chain atoms of Gly19 and Ala20 adopt distinct alternative conformations. The benzyl side chain and the proline ring of the Suc-AAPF-CMK inhibitor are very well defined in the S1 and S2 pockets, whereas two alternate conformations are observed for the main and side chain of Ala in P3 position, as well as two conformations of the succinyl carboxylate, which are rotated against each other by ≈60° (Fig. 3 The Structural Basis of Zinc and Copper Ion Inhibition. Soaking with Zn2+ resulted in the destruction of hK7 inhibitor complex crystals, but a corresponding experiment with Cu2+ yielded crystals that diffracted to 2.0 Å resolution, although the cell constants changed significantly (Table 1). In the 2Fo − Fc electron density map, two peaks with strong density were identified and built in the model as Cu2+ ions. The first one (Cu1) is coordinated by the Nε2 of His99 via a water molecule by the main-chain carbonyl of Thr96, and two additional water molecules, whereas the second (Cu2) appears to be only bound by the Nδ1 of His41 and a single water molecule. Both sites displayed peaks in an anomalous Fourier map, as expected for transition metal ions, but the one for Cu1 was much stronger (Fig. 5
Conclusion Apparently, hK7 resembles more hK1, hK4, and hK6 than, for example, chymotrypsin, whereas its specificity can be classified as modified chymotrypsin-like with a unique P1 and P2 preference for Tyr (19). At S2, hK7 prefers Tyr over medium-sized hydrophobic and polar residues. Also, the S1 pocket of hK7 is more specific for Tyr than for Phe, Ala, or Met residues, which is mostly explained by the polar Asn189 at the bottom of the overall hydrophobic S1 pocket (Fig. 4 The major Zn2+ inhibition site of hK7 has been unambiguously identified at His99 by the comparison of the H99A and H41F mutant inhibition kinetics. Despite the presence of only a second potential His ligand for Zn2+ (Fig. 5 Also, hK7 has been implicated in skin diseases and progression of ovarian and other cancer types. Thus, a better understanding of the hK7 enzymatic activity including the zinc inhibition based on our high-resolution structure could lead to the synthesis of selective small molecule inhibitors as antiinflammatory and potent anticancer therapeutics. Materials and Methods Purification of hK7. One form of recombinant hK7 was expressed in a baculovirus-insect cell system as a fusion protein with the segments ubiquitin, an enterokinase (EK) cleavage site, and mature hK7, as reported previously (20). Active hK7I was generated by removal of the ubiquitin tag with EK. Subsequently, hK7I was purified by affinity chromatography on a phenylbutylamine–Affi-Gel 10 resin followed by chromatography on heparin–Sepharose. The second recombinant form, hK7E, was expressed in E. coli as inclusion bodies, refolded from urea, activated by cleavage of an artificial N terminus by EK, and purified as described previously (19). Mutagenesis was performed with mutated primers by PCR with Pfu Turbo (Stratagene, La Jolla, CA) and the original plasmid as template, which was afterward digested by DpnI (New England Biolabs, Ipswich, MA). The hK7E mutant proteins H41F and H99A were prepared according to protocol for the wild type. Enzyme Kinetics. The hK7 activity was determined with the substrates Phe-AMC, Tyr-AMC, and Suc-LLY-AMC (Bachem, Bubendorf, Switzerland) ranging from 10 to 150 μM. Kinetic parameters of hK7 were determined in 50 mM Hepes, pH 7.5/150 mM NaCl/0.005% Tween 20 at 25°C from the initial velocity of the substrate cleavage at 221 nM concentration of hK7, whereas for the measurement series concerning the inhibition type 50 nM hK7 was used. The signal of the released AMC was fluorometrically recorded at excitation and emission wavelengths of 360 and 420 nm, respectively. The fraction of active hK7 was measured by active-site titration with standardized bovine trypsin inhibitor as described previously (29) and Suc-LLY-AMC (Bachem) as substrate. Kinetic data were analyzed with Origin (OriginLab, Northampton, MA). The inhibition curve was measured at 25°C for an hK7 concentration of 100 nM with 85 μM Suc-AAPF-AMC in 100 mM Tris·HCl, pH 8.0/200 mM NaCl/9% DMSO with CuCl2 and ZnCl2 added in the range from 0.2 to 200 and 500 μM, respectively (excitation at 370 nm and emission at 475 nm). For calculation of the inhibition constant Ki(app) the following formula was used:
Crystallization, Data Collection, and Refinement. The two recombinant hK7 species, complexed with the inhibitors AAF-CMK and Suc-AAPF-CMK, yielded different crystal forms at 18°C by the sitting-drop vapor diffusion method. Crystal form 1 grew in drops of 1 μl of protein solution (7 mg/ml hK7E-AAF-CMK complex) and 1 μl of 100 mM [bis(2-hydroxyethyl)amino]tris(hydroxy methyl) methane·HCl, pH 6.0/ 25% PEG 3350/2.5 M Li2SO4, equilibrated against 500 μl of reservoir buffer. These crystals were mounted under a nitrogen gas stream at 100 K and diffracted beyond 2.0 Å resolution at the synchrotron (beamline BW6; DESY, Hamburg, Germany). They belong to the monoclinic space group P21 and contain two monomers per asymmetric unit (see Table 1). The crystals of the hK7I-Suc-AAPF-CMK complex were grown from 2.5 μl of protein solution and 1.5 μl of 100 mM sodium cacodylate, pH 6.5/200 mM magnesium acetate/30% (vol/vol) 2-methyl-2,4-pentanediol with 500 μl of reservoir buffer. The hK7I-Suc-AAPF-CMK crystals were transferred to crystallization buffer with 20% glycerol and diffracted beyond 1.0 Å resolution (BW6). Two datasets for low- and high-resolution data were collected. These crystals belonged to the space group P21 with one molecule per asymmetric unit, but they changed their cell constants significantly upon soaking with 10 mM CuSO4 solution (Table 1). These data were evaluated with MOSFLM (42) and scaled with SCALA (www.ccp4.ac.uk/ccp4I_main.php) and DENZO/SCALEPACK (35), respectively. Molecular replacement searches were performed with PHASER (36) by using the coordinates of hK6 [Protein Data Bank (PDB) ID code 1LO6]. In the case of hK7E-AAF-CMK, the best solution had a log-likelihood gain (LLG) of +266 and Z values for the rotation function (RFZ) of 7.3 and of 15.4 for the translation function (TFZ), whereas the best solution for hK7I-AAPF-CMK reached a LLG of +147 with Z values of RFZ = 8.1 and TFZ = 7.1. For hK7I-Suc-AAPF-CMK-Cu using the refined hK7I-Suc-AAPF-CMK model, PHASER found a solution with a LLG of +1,617 and Z values of RFZ = 34.2 and TFZ = 34.1. The correctness of the replacement solutions was validated by inspecting the packing of symmetry-related molecules and with composite omit maps calculated in CNS (43). Model building for hK7E-AAF-CMK was performed with the program O and refinement with CNS, resulting in final Rcryst and Rfree values of 26.6% and 29.2%, respectively, for a maximum resolution of 2.6 Å (Table 1). Several cycles of refinement in CNS and model building for hK7I-Suc-AAPF-CMK with MAIN (44) and CNS, using standard target values (37), resulted in final Rcryst and Rfree of 18.0% and 23.3% for data to 2.0 Å (Table 1). The whole main chain of the hK7 catalytic domain is well defined by electron density, except for a few side chains whose occupancy was set at zero. The copper-containing hK7I-Suc-AAPF-CMK-CU model was refined to Rcryst and Rfree of 21.7% and 25.1%, respectively, at 2.1 Å resolution. For the high-resolution structure of hK7I-Suc-AAPF-CMK, the refined 2.0 Å model was used for rigid body and conjugate gradient refinement with SHELX-97 (http://shelx.uni-ac.gwdg.de/) to 1.5 Å. Alternate conformations were built including multiple positions of water molecules with XTALVIEW (www.sdsc.edu/CCMS/Packages/XTALVIEW/xtalview.html) and COOT (38). Subsequently, anisotropic B factors and occupancies of alternate atom positions were refined to 1.0 Å resolution. In the final refinement cycles, the riding hydrogen model was used, resulting in Rcryst of 13.1% and an Rfree of 15.9%. All figures were created with PMOL version 0.98 (39), whereas the potential phi map was calculated with GRASP (40). Acknowledgments We are thankful to R. Faessler for support of this work and to G. Bourenkov and G. Kalachova for help with data collection. We are grateful to Zhi-Mei Wang and Eun-Jung Choi for the preparation of recombinant hK7I. This work was supported by the European Commission (CAMP; LSHG-2006–018830), by the Fonds der Chemischen Industrie (to W.B.), by the Kommission Klinische Forschung der TU München (to V.M.), and by the Graduiertenkolleg 333 der Deutschen Forschungsgemeinschaft (to M.D.). Abbreviations Footnotes The authors declare no conflict of interest. Data deposition: The atomic coordinates and structure factors have been deposited in the Protein Data Bank, www.pdb.org (PDB ID codes 2QXG, 2QXH, 2QXI, and 2QXJ). References 1. Egelrud T, Hofer PA, Lundstrom A. Acta Derm Venereol. 1988;68:93–97. [PubMed] 2. Egelrud T. J Invest Dermatol. 1993;101:200–204. [PubMed] 3. Egelrud T, Lundstrom A. Arch Dermatol Res. 1991;283:108–112. [PubMed] 4. Caubet C, Jonca N, Brattsand M, Guerrin M, Bernard D, Schmidt R, Egelrud T, Simon M, Serre G. J Invest Dermatol. 2004;122:1235–1244. [PubMed] 5. 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Acta Derm Venereol. 1988; 68(2):93-7.
[Acta Derm Venereol. 1988]J Invest Dermatol. 1993 Aug; 101(2):200-4.
[J Invest Dermatol. 1993]Arch Dermatol Res. 1991; 283(2):108-12.
[Arch Dermatol Res. 1991]J Invest Dermatol. 2004 May; 122(5):1235-44.
[J Invest Dermatol. 2004]Br J Dermatol. 2005 Dec; 153(6):1200-3.
[Br J Dermatol. 2005]J Invest Dermatol. 1993 Aug; 101(2):200-4.
[J Invest Dermatol. 1993]Arch Dermatol Res. 1991; 283(2):108-12.
[Arch Dermatol Res. 1991]J Invest Dermatol. 2004 May; 122(5):1235-44.
[J Invest Dermatol. 2004]Arch Dermatol Res. 1999 Apr; 291(4):195-200.
[Arch Dermatol Res. 1999]Br J Dermatol. 2005 Dec; 153(6):1200-3.
[Br J Dermatol. 2005]Arch Dermatol Res. 1999 Apr; 291(4):195-200.
[Arch Dermatol Res. 1999]J Invest Dermatol. 2002 Mar; 118(3):444-9.
[J Invest Dermatol. 2002]J Cutan Pathol. 2003 Jul; 30(6):358-62.
[J Cutan Pathol. 2003]Acta Derm Venereol. 2003; 83(5):322-7.
[Acta Derm Venereol. 2003]J Transl Med. 2005 Jun 21; 3():25.
[J Transl Med. 2005]Int J Gynecol Cancer. 2001 Nov-Dec; 11(6):454-61.
[Int J Gynecol Cancer. 2001]Clin Cancer Res. 2005 May 1; 11(9):3446-54.
[Clin Cancer Res. 2005]Clin Cancer Res. 2003 May; 9(5):1710-20.
[Clin Cancer Res. 2003]Cancer. 1999 Nov 15; 86(10):2074-82.
[Cancer. 1999]J Biol Chem. 2006 Sep 1; 281(35):25678-88.
[J Biol Chem. 2006]Biol Chem. 2005 Nov; 386(11):1173-84.
[Biol Chem. 2005]J Mol Biol. 1983 Feb 25; 164(2):237-82.
[J Mol Biol. 1983]J Mol Biol. 1978 Jan 5; 118(1):99-112.
[J Mol Biol. 1978]J Mol Biol. 1983 Feb 25; 164(2):237-82.
[J Mol Biol. 1983]FEBS Lett. 1975 Aug 1; 56(1):139-43.
[FEBS Lett. 1975]Protein Sci. 1992 Apr; 1(4):426-71.
[Protein Sci. 1992]Biochem Biophys Res Commun. 1967 Apr 20; 27(2):157-62.
[Biochem Biophys Res Commun. 1967]Proteins. 2005 Mar 1; 58(4):802-14.
[Proteins. 2005]J Mol Biol. 2006 Oct 6; 362(5):1094-107.
[J Mol Biol. 2006]Biochemistry. 1991 May 28; 30(21):5217-25.
[Biochemistry. 1991]J Biol Chem. 2006 Sep 1; 281(35):25678-88.
[J Biol Chem. 2006]Acta Crystallogr D Biol Crystallogr. 1994 Mar 1; 50(Pt 2):178-85.
[Acta Crystallogr D Biol Crystallogr. 1994]J Mol Biol. 1987 May 20; 195(2):373-96.
[J Mol Biol. 1987]Biochemistry. 1993 Mar 2; 32(8):1914-9.
[Biochemistry. 1993]J Biol Chem. 2006 Sep 1; 281(35):25678-88.
[J Biol Chem. 2006]J Histochem Cytochem. 2004 Apr; 52(4):529-39.
[J Histochem Cytochem. 2004]Biol Chem. 2005 Nov; 386(11):1173-84.
[Biol Chem. 2005]Nat Genet. 2005 Jan; 37(1):56-65.
[Nat Genet. 2005]Biol Chem. 2005 Nov; 386(11):1173-84.
[Biol Chem. 2005]J Biol Chem. 2006 Sep 1; 281(35):25678-88.
[J Biol Chem. 2006]J Mol Biol. 2006 Oct 6; 362(5):1094-107.
[J Mol Biol. 2006]Acta Crystallogr D Biol Crystallogr. 2005 Apr; 61(Pt 4):458-64.
[Acta Crystallogr D Biol Crystallogr. 2005]Acta Crystallogr D Biol Crystallogr. 1998 Sep 1; 54(Pt 5):905-21.
[Acta Crystallogr D Biol Crystallogr. 1998]Acta Crystallogr D Biol Crystallogr. 2004 Dec; 60(Pt 12 Pt 1):2126-32.
[Acta Crystallogr D Biol Crystallogr. 2004]Proteins. 1991; 11(4):281-96.
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