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Three-Dimensional Structure of a Mammalian Thioredoxin Reductase: Implications for Mechanism and Evolution of a Selenocysteine-Dependent Enzyme

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Three-Dimensional Structure of a Mammalian Thioredoxin Reductase: Implications for Mechanism and Evolution of a Selenocysteine-Dependent Enzyme Three-dimensional structure of a mammalian thioredoxin reductase: Implications for mechanism and evolution of a selenocysteine-dependent enzyme Tatyana Sandalova*, Liangwei Zhong†, Ylva Lindqvist*, Arne Holmgren†, and Gunter Schneider*‡ *Division of Molecular Structural Biology and †Medical Nobel Institute for Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden Edited by David R. Davies, National Institutes of Health, Bethesda, MD, and approved June 15, 2001 (received for review April 5, 2001) Thioredoxin reductases (TrxRs) from mammalian cells contain an are inhibited by a number of clinically used drugs (review in essential selenocysteine residue in the conserved C-terminal se- ref. 12). quence Gly-Cys-SeCys-Gly forming a selenenylsulfide in the oxi- Cloning and sequencing of a putative human (13) and the dized enzyme. Reduction by NADPH generates a selenolthiol, bovine and rat cytosolic TrxR (14) revealed that they are similar which is the active site in reduction of Trx. The three-dimensional to GR and not to the Escherichia coli TrxR enzyme. Compared structure of the SeCys498Cys mutant of rat TrxR in complex with with GR, the polypeptide chain of rat TrxR contains a C- -NADP؉ has been determined to 3.0-Å resolution by x-ray crystal- terminal extension of 16 residues carrying a penultimate seleno lography. The overall structure is similar to that of glutathione cysteine residue in the conserved sequence motif Gly-Cys- reductase (GR), including conserved amino acid residues binding SeCys-Gly (14, 15). The selenocysteine residue is essential the cofactors FAD and NADPH. Surprisingly, all residues directly because its replacement with cysteine results in a mutant rat interacting with the substrate glutathione disulfide in GR are TrxR enzyme with about 1% activity with Trx as substrate and conserved despite the failure of glutathione disulfide to act as a with a major loss in kcat (11). Other activities of Se-containing BIOCHEMISTRY TrxR and reduction of lipid hydroperoxides and H O are lost in substrate for TrxR. The 16-residue C-terminal tail, which is unique 2 2 the Cys mutant, indicating an absolute requirement of selenium to mammalian TrxR, folds in such a way that it can approach the for these reactions. Because of the high nucleophilicity of active site disulfide of the other subunit in the dimer. A model of selenolate, it is more susceptible to oxidation by H2O2 than the complex of TrxR with Trx suggests that electron transfer from thiols, a property that allows extension of the substrate spectrum NADPH to the disulfide of the substrate is possible without large toward hydroperoxides in the mammalian enzymes (11). conformational changes. The C-terminal extension typical of mam- The truncated enzyme lacking the SeCys-Gly dipeptide is malian TrxRs has two functions: (i) it extends the electron transport folded and contains FAD but is inactive, although titrations with chain from the catalytic disulfide to the enzyme surface, where it NADPH yield the characteristic red-shifted thiolate-flavin can react with Trx, and (ii) it prevents the enzyme from acting as charge transfer complex common for GR and mammalian TrxR a GR by blocking the redox-active disulfide. Our results suggest (11, 16). Recently, the active site of mammalian TrxR was that mammalian TrxR evolved from the GR scaffold rather than identified as a selenenylsulfide in the oxidized enzyme, and a from its prokaryotic counterpart. This evolutionary switch renders selenolthiol is formed from the conserved Cys-SeCys sequence cell growth dependent on selenium. (17). The selenenyl sulfides in the oxidized human enzyme also have been confirmed (18). hioredoxin reductase (TrxR) (EC 1.6.4.5) is a member of the TrxRs from mammalian sources belong to the rare group of enzymes containing selenocysteine, and few crystallographic pyridine nucleotide–disulfide oxidoreductase family (1). En- T studies of such enzymes have been performed, e.g., glutathione zymes of this family, such as glutathione reductase (GR), peroxidase (19) and formate dehydrogenase H (20). Here, we lipoamide dehydrogenase, and trypanothione reductase, form report the three-dimensional structure of the SeCys498Cys homodimers, and each subunit contains a redox-active disulfide mutant of rat TrxR complexed with NADPϩ. The crystal struc- bond and a tightly bound FAD molecule. TrxR catalyzes reduc- ture analysis reveals the overall fold of the enzyme, provides tion of Trx by NADPH. Trx is a ubiquitous 12-kDa protein, which insights into the architecture of the active site, and allows a in its dithiol form is the major disulfide reductase in cells (2, 3). detailed comparison to other members of the pyridine nucleo- Mammalian Trx is an essential protein (4) with a large number tide disulfide oxidoreductase family. of functions in cell growth, such as thiol redox control of transcription factors, electron transport to ribonucleotide reduc- Materials and Methods tase, or defense against oxidative stress and apoptosis (2, 3). Trx Protein Purification and Crystallization. Purification and crystalli- and TrxR are present in all living cells from archea to human (3, zation of the SeCys498Cys mutant of rat TrxR in the presence of 5). Whereas the essential features of Trx have been conserved NADPϩ was carried out as described (21). during evolution, mammalian TrxRs are very different in struc- ture and properties from the enzymes in bacteria, fungi, and plants (5, 6). For instance, mammalian TrxRs have a higher This paper was submitted directly (Track II) to the PNAS office. molecular mass (Ն55 kDa) and a very broad substrate specificity Abbreviations: Trx, thioredoxin; TrxR, thioredoxin reductase; GR, glutathione reductase; GSSG, glutathione disulfide. (7) in contrast to the smaller (35 kDa) specific enzymes repre- Data deposition: The crystallographic data for rat thioredoxin reductase have been depos- sented by the well characterized Escherichia coli TrxR (8). ited in the Protein Data Bank, www.rcsb.org (PDB ID code 1H6V). Mammalian TrxR directly reduces not only Trx from different ‡To whom reprint requests should be addressed. E-mail: [email protected]. species but also many nondisulfide substrates such as selenite (9), The publication costs of this article were defrayed in part by page charge payment. This lipid hydroperoxides (10), and H2O2 (11) but not glutathione article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. disulfide (GSSG) (5–7). Furthermore, the mammalian enzymes §1734 solely to indicate this fact. www.pnas.org͞cgi͞doi͞10.1073͞pnas.171178698 PNAS ͉ August 14, 2001 ͉ vol. 98 ͉ no. 17 ͉ 9533–9538 Downloaded by guest on September 26, 2021 Table 1. Data collection and refinement statistics above all others, giving three dimers in the asymmetric unit with ϭ Resolution (Å) 30.0–3.0 (3.05–3.0) a correlation coefficient of 0.41 and r 53.4% and perfect Number of observations 212,337 crystal packing. The next best solution had a correlation coef- ϭ Number of unique reflections 69,351 ficient of 0.354 and r 56%. ͗I͞␴I͘ 11.0 (2.1) The coenzymes had been excluded from the search model, and Completeness 92.7 (77.6) the correctness of the molecular replacement solution was R 9.5 (44.8) confirmed by electron density for FAD and the 2Јphospho-AMP sym ϩ Refinement statistics moiety of NADP appearing at the expected positions. Refine- Number of atoms 23,104 ment was performed with CNS (24). Five percent of the data were Rfactor 0.230 selected to monitor the progress of refinement by calculation of Rfree 0.264 Rfree. Manual rebuilding of the model was performed with the 2 ␴ Ϫ Ϫ Overall B factor (Å ) 22.5 program O (25) based on A-weighted 2Fo Fc and Fo Fc Average B factor for C-terminal 16 residues (Å2) 29.7 electron density maps. rms deviation bonds 0.013 The electron density maps suggested that a tryptophan residue rms deviation angles 1.970 should replace Gly-53, which was confirmed by reexamination of Ramachandran plot, nonglycine residues in: the original sequencing data (14). Refinement continued with Most favorable regions (%) 82.9 REFMAC5 (26), where the six subunits were considered as dif- ͞ ͞ Additional allowed regions (%) 17.1 ferent TLS groups resulting in Rfree R values of 26.4 23.0%, Disallowed regions (%) 0.0 respectively. Restrained noncrystallographic symmetry (CNS͞ Ϫ Ϫ REFMAC; 100 kcal⅐mol 1⅐Å 2͞0.05 Å for main chain, and 50 kcal⅐molϪ1⅐ÅϪ2͞0.5 Å for side-chain atoms) was used in the Crystallographic Data Collection. X-ray data from a single crystal refinement. were collected to 3.0-Å resolution on a MAR345 image plate at Structural comparisons were carried out by using the program a temperature of 100 K and a wavelength of 1.104 Å at the TOP with default parameters (27). Modeling of the binding of Trx synchrotron beamline I711 (MAX Laboratory, Lund University, to TrxR was performed manually with O (25). Figures were made Sweden). Crystallization buffer containing 20% ethylene glycol with MOLSCRIPT (28), BOBSCRIPT (27), and RASTER3D (29, 30). was used as cryoprotectant. The x-ray data were processed and Results scaled with the HKL suite (22), and the statistics of the data set are given in Table 1. The crystals belong to the monoclinic space Electron Density Map and Quality of the Model. The asymmetric unit ϭ ϭ ϭ group P21 with cell dimensions a 78.9 Å, b 140.5 Å, c 170.8 of the crystal contains three dimers of rat TrxR. With a few Å, and ␤ ϭ 94.6°. exceptions, all polypeptide chains are well defined in electron density. The real space fit correlation to the electron density map Molecular Replacement and Crystallographic Refinement. A dimer of is in the range 0.75 to 0.8 for all subunits except subunit C, where GR from human erythrocytes (PDB accession code 1GRA), it is slightly less at 0.7.
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