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A Model for the Reaction Mechanism of the Transglutaminase 3 Enzyme

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A Model for the Reaction Mechanism of the Transglutaminase 3 Enzyme EXPERIMENTAL and MOLECULAR MEDICINE, Vol. 35, No. 4, 228-242, August 2003 A model for the reaction mechanism of the transglutaminase 3 enzyme Bijan Ahvazi1,3 and Peter M. Steinert 2* Introduction 1Laboratory of X-ray Crystallography Facility/ Transglutaminases (TGase; protein-glutamine: amine Office of Science and Technology γ-glutamyl-transferase) are a family of calcium-dependent 2Laboratory of Skin Biology acyl-transfer enzymes that are widely expressed in bi- National Institute of Arthritis and ota (Folk and Chung, 1985; Greenberg et al., 1991; Musculoskeletal and Skin Diseases Melino et al., 1998; Melino et al., 2000; Fesus and National Institutes of Health Piacentini, 2002). Each of the eight active human Bethesda, MD 20892-8023, U.S.A. TGase enzyme isoforms can activate a protein-bound 3Corresponding author: Tel, 301-402-4086; Gln residue to form a thiol-acyl enzyme intermediate, Fax, 301-480-0742; E-mail, [email protected] which is attacked by a second nucleophilic substrate *Deceased April 7, 2003. to accomplish the two-step reaction. The reaction leads to the formation of an isopeptide bond between two Accepted 13 August 2003 proteins and the covalent incorporation of polyamine into protein (Folk and Chung, 1985; Greenberg et al., Abbreviations: fTG, fish TGase; fXIIIa, blood clotting factor XIIIa; 1991). The nucleophile may be: water, so that the ac- tivated Gln residue is deamidated to a Glu; a poly- TGase, transglutaminase amine, so that a mono-substituted adduct or bi-substi- tuted cross-link is formed; an alcohol, particularly the ω-hydroxyl group of certain long-chain ceramides ex- Abstract pressed in mammalian epidermis, to form an ester; and perhaps most commonly, an ε-NH2 group of a Transglutaminase enzymes (TGases) catalyze the protein bound Lys residue, resulting in the formation ε calcium dependent formation of an isopeptide bond of an N -(γ-glutamyl)lysine isopeptide cross-link (Nemes between protein-bound glutamine and lysine sub- et al., 1999; Nemes et al., 2000). This stabilizes macro- strates. Previously we have shown that activated molecular protein complexes. Typically, TGases rec- TGase 3 acquires two additional calcium ions at ognize the generic sequence motif Gln-Gln*-Val for site two and three. The calcium ion at site three the first step of the reaction (where Gln* represents results in the opening of a channel. At this site, the targeted residue), although different isoforms dis- the channel opening and closing could modulate, play specificity as to which substrates bearing the depending on which metal is bound. Here we pro- motif may approach the enzyme (Nemes et al., 1999). pose that the front of the channel could be used Anecdotal data suggest less specificity for Lys sub- by the two substrates for enzyme reaction. We strates (Tarcsa et al., 1998; Candi et al., 1999; Nemes propose that the glutamine substrate is directed et al., 1999). The three dimensional structures of four TGases from Trp236 into the enzyme, shown by molecular docking. Then a lysine substrate approaches the have now been reported, i.e. human factor XIIIa (hfXIIIa) opened active site to engage Trp327, leading to (Yee et al., 1994), TGase 2 (Liu et al., 2002), TGase 3 enzymes (Ahvazi et al., 2002; 2003), and a fish formation of the isopeptide bond. Further, direct enzyme (fTG, equivalent to mammalian TGase 2, comparisons of the structures of TGase 3 with Noguchi et al., 2001). All consist of four domains that other TGases have allowed us to identify several are similar in organization and fold (Figure 1a, b for residues that might potentially be involved in ge- TGase 3): the amino terminal β-sandwich domain; the neric and specific recognition of the glutamine and catalytic core domain which contains the conserved lysine substrates. active site triad of Cys272, His330 and Asp353 (using TGase 3 residue numbers); the β-barrel 1 domain; Keywords: calcium ions; protein structure; residue spe- and the β-barrel 2 domain at the carboxy terminus. cificity; TGase; TGase mechanism; X-ray crystallography FXIIIa and TGase 3 are zymogens that require proteolytic cleavage at different sites for activation, whereas most other such enzymes are constitutively active. Model mechanism of transglutaminase 3 enzyme 229 Figure 1. (A) The solved structure of activated human TGase 3 in presence of Ca2+ ions. The four domains and Ca2+ ions are shown. The electrostatic potential has been mapped onto the surface plan from -12.0 kT (deep red, acidic) to +12.0 kT (deep blue, basic). The β-octylglucoside molecule is shown as ball and stick. The catalytic triad residues Cys272, His330, and Asp353 and location of the three Ca2+ ions are shown in yellow. (B) Stereo views of the electrostatic surface potential (black transparent) show that the active site triad residues Cys272, His330 and Asp353 are buried and inaccessible. (C) The connolly surface channel is shown in the active form. The move- ment of the loop bearing residues Asp320-Ser325 opens the channel in the activated TGase 3, and exposes the side chains of the Trp236 and Trp327 residues. 230 Exp. Mol. Med. Vol. 35(4), 228-242, 2003 One intriguing feature of TGases is their rather gen and the activated forms of TGase 3, as well as slow rate of reaction. When measured using either an molecular modeling of Gln and Lys substrates, we artificial substrate such as methylated casein or the present here a new model for its mechanism of action known favored substrate loricrin, the fastest rate of that may offer clues as to how TGase 3 specificity reaction of activated TGase 1 or 3 enzymes that has is determined. been measured is about 1,000 pmol of incorporated putrescine/hour/pmol of enzyme, which corresponds to one reaction cycle per 3-4 seconds (Kim et al., Extant Concepts for TGase 1994; Candi et al., 1998). TGase 2 is comparably slow Reaction Mechanism (Kim et al., 1994). However, the structural features that determine substrate specificity and this very mo- In the available X-ray structures of TGase 3 (Ahvazi dest rate of reaction remain largely unexplored. In et al., 2002; Ahvazi et al., 2003), the catalytic triad addition, the solved TGase structures reveal the pre- active residues, including Cys272 at the active site, sence of three unusual cis peptide bonds located in are buried in the hydrophobic interior of the enzyme. the catalytic core domain in motifs that flank the ac- The sulfhydryl group of Cys272 forms an intimate tive site triad residues. Typically such bonds are ener- thiolate-imidazolium ion pair with His330. The imino getically unfavorable and are thought to be present nitrogen atom of the His330 ring forms a hydrogen in proteins because they are required for some aspect bond with the terminal oxygen atom of Asp353. In of the reaction mechanism cycle and/or confer special addition, the hydroxyl of Tyr525 is within hydrogen stability (Weiss et al., 1998; Jabs et al., 1999). bonding distance of Cys272 and Trp236 and is locat- One of the most enigmatic aspects of catalysis by ed at the loop of the sequence motif Ile523-Asn526 the TGases is that all are Ca2+ ion dependent for both of the β-barrel domain 1 that occludes the entrance in vivo (Folk and Chung, 1985) and in vitro reactions to the active site (Figure 2a). These bonds must be (Fox et al., 1999; Ahvazi et al., 2002; Ahvazi et al., cleaved and structural motifs near the enzyme's sur- 2003), although few data are currently available on face must be moved to allow substrates to approach how or why their dependence on Ca2+ metal ions is the active site to effect reaction. Also, there is evi- necessary. For example, the solved X-ray structures dence that two tryptophan residues (Trp236 and of the zymogen forms of hfXIIIa with or without a Trp327), the indole rings of which are buried near the single Ca2+ ion do not reveal any structural changes surface, are intimately involved in the enzyme reac- (Yee et al., 1994; Yee et al., 1996; Fox et al., 1999). tion mechanism by forming an oxyanion intermediate Furthermore, the structures of the fTG (Noguchi et al., first with the glutamine substrate and then with the 2001) and human TGase 2 (Liu et al., 2002) enzymes lysine substrate, in order to form the isopeptide cross- do not show any bound metal Ca2+ ion. In our link bond (Pedersen et al., 1994). Thus one early sug- comparison of the zymogen and activated TGase 3 gestion for a possible TGase enzyme mechanism is enzyme we found that the zymogen possesses one predicted that substrates should approach from the tightly bound Ca2+ ion (PDB 1L9M) in site one but front side of the enzyme, dislodge some portion of the proteolyzed form becomes active only after the the protein surface to expose the two Trp residues exothermic binding of two more Ca2+ ions (PDB 1L9N) and break the hydrogen bonds masking the active in sites two and three (Ahvazi et al., 2002). Notably, site Cys residue (Yee et al., 1994; Noguchi et al., the local environment of the metal ion binding sites 2001). The importance of these two Trp residues has change upon Ca2+ ion chelation. A loop at the 'front' recently been confirmed (Murthy et al., 2002). Further- of the enzyme moves about 9 Å so that the side chain more, the likely importance of the cis peptide bonds of Asp324 can coordinate with the Ca2+ ion in site has been discussed (Weiss et al., 1998; Jabs et al., three, and this opens a channel that passes through 1999). However, no further details or comprehensive the activated enzyme just below the buried active site suggestions have been advanced to date that could (Figure 1b and 1c; Ahvazi et al., 2002; Ahvazi et al., accommodate all of these observations, and the pre- 2003).
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