1
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Zhang W, Niu X, Ding J, Hu Y, Jin C. Intra- and inter-protein couplings of backbone motions underlie protein thiol-disulfide exchange cascade. Sci Rep 2018; 8:15448. [PMID: 30337655 PMCID: PMC6193951 DOI: 10.1038/s41598-018-33766-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/06/2018] [Indexed: 11/09/2022] Open
Abstract
The thioredoxin (Trx)-coupled arsenate reductase (ArsC) is a family of enzymes that catalyzes the reduction of arsenate to arsenite in the arsenic detoxification pathway. The catalytic cycle involves a series of relayed intramolecular and intermolecular thiol-disulfide exchange reactions. Structures at different reaction stages have been determined, suggesting significant conformational fluctuations along the reaction pathway. Herein, we use two state-of-the-art NMR methods, the chemical exchange saturation transfer (CEST) and the CPMG-based relaxation dispersion (CPMG RD) experiments, to probe the conformational dynamics of B. subtilis ArsC in all reaction stages, namely the enzymatic active reduced state, the intra-molecular C10-C82 disulfide-bonded intermediate state, the inactive oxidized state, and the inter-molecular disulfide-bonded protein complex with Trx. Our results reveal highly rugged energy landscapes in the active reduced state, and suggest global collective motions in both the C10-C82 disulfide-bonded intermediate and the mixed-disulfide Trx-ArsC complex.
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Affiliation(s)
- Wenbo Zhang
- College of Life Sciences, Peking University, Beijing, 100871, China.,Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China
| | - Xiaogang Niu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.,Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China
| | - Jienv Ding
- College of Life Sciences, Peking University, Beijing, 100871, China.,Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China.,National Institutes of Health, DHHS 1050 Boyles Street, Frederick, MD, 21702, USA
| | - Yunfei Hu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China. .,Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China. .,Medical College of Soochow University, Suzhou, 215123, China.
| | - Changwen Jin
- College of Life Sciences, Peking University, Beijing, 100871, China. .,College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China. .,Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, 100871, China. .,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China.
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2
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Ronchi VP, Kim ED, Summa CM, Klein JM, Haas AL. In silico modeling of the cryptic E2∼ubiquitin-binding site of E6-associated protein (E6AP)/UBE3A reveals the mechanism of polyubiquitin chain assembly. J Biol Chem 2017; 292:18006-18023. [PMID: 28924046 DOI: 10.1074/jbc.m117.813477] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Indexed: 12/13/2022] Open
Abstract
To understand the mechanism for assembly of Lys48-linked polyubiquitin degradation signals, we previously demonstrated that the E6AP/UBE3A ligase harbors two functionally distinct E2∼ubiquitin-binding sites: a high-affinity Site 1 required for E6AP Cys820∼ubiquitin thioester formation and a canonical Site 2 responsible for subsequent chain elongation. Ordered binding to Sites 1 and 2 is here revealed by observation of UbcH7∼ubiquitin-dependent substrate inhibition of chain formation at micromolar concentrations. To understand substrate inhibition, we exploited the PatchDock algorithm to model in silico UbcH7∼ubiquitin bound to Site 1, validated by chain assembly kinetics of selected point mutants. The predicted structure buries an extensive solvent-excluded surface bringing the UbcH7∼ubiquitin thioester bond within 6 Å of the Cys820 nucleophile. Modeling onto the active E6AP trimer suggests that substrate inhibition arises from steric hindrance between Sites 1 and 2 of adjacent subunits. Confirmation that Sites 1 and 2 function in trans was demonstrated by examining the effect of E6APC820A on wild-type activity and single-turnover pulse-chase kinetics. A cyclic proximal indexation model proposes that Sites 1 and 2 function in tandem to assemble thioester-linked polyubiquitin chains from the proximal end attached to Cys820 before stochastic en bloc transfer to the target protein. Non-reducing SDS-PAGE confirms assembly of the predicted Cys820-linked 125I-polyubiquitin thioester intermediate. Other studies suggest that Glu550 serves as a general base to generate the Cys820 thiolate within the low dielectric binding interface and Arg506 functions to orient Glu550 and to stabilize the incipient anionic transition state during thioester exchange.
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Affiliation(s)
| | - Elizabeth D Kim
- From the Department of Biochemistry and Molecular Biology and
| | - Christopher M Summa
- the Department of Computer Science, University of New Orleans, New Orleans, Louisiana 70148
| | | | - Arthur L Haas
- From the Department of Biochemistry and Molecular Biology and .,the Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana 70112 and
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3
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Rosado LA, Wahni K, Degiacomi G, Pedre B, Young D, de la Rubia AG, Boldrin F, Martens E, Marcos-Pascual L, Sancho-Vaello E, Albesa-Jové D, Provvedi R, Martin C, Makarov V, Versées W, Verniest G, Guerin ME, Mateos LM, Manganelli R, Messens J. The antibacterial prodrug activator Rv2466c is a mycothiol-dependent reductase in the oxidative stress response of Mycobacterium tuberculosis. J Biol Chem 2017; 292:13097-13110. [PMID: 28620052 DOI: 10.1074/jbc.m117.797837] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/12/2017] [Indexed: 12/19/2022] Open
Abstract
The Mycobacterium tuberculosis rv2466c gene encodes an oxidoreductase enzyme annotated as DsbA. It has a CPWC active-site motif embedded within its thioredoxin fold domain and mediates the activation of the prodrug TP053, a thienopyrimidine derivative that kills both replicating and nonreplicating bacilli. However, its mode of action and actual enzymatic function in M. tuberculosis have remained enigmatic. In this study, we report that Rv2466c is essential for bacterial survival under H2O2 stress. Further, we discovered that Rv2466c lacks oxidase activity; rather, it receives electrons through the mycothiol/mycothione reductase/NADPH pathway to activate TP053, preferentially via a dithiol-disulfide mechanism. We also found that Rv2466c uses a monothiol-disulfide exchange mechanism to reduce S-mycothiolated mixed disulfides and intramolecular disulfides. Genetic, phylogenetic, bioinformatics, structural, and biochemical analyses revealed that Rv2466c is a novel mycothiol-dependent reductase, which represents a mycoredoxin cluster of enzymes within the DsbA family different from the glutaredoxin cluster to which mycoredoxin-1 (Mrx1 or Rv3198A) belongs. To validate this DsbA-mycoredoxin cluster, we also characterized a homologous enzyme of Corynebacterium glutamicum (NCgl2339) and observed that it demycothiolates and reduces a mycothiol arsenate adduct with kinetic properties different from those of Mrx1. In conclusion, our work has uncovered a DsbA-like mycoredoxin that promotes mycobacterial resistance to oxidative stress and reacts with free mycothiol and mycothiolated targets. The characterization of the DsbA-like mycoredoxin cluster reported here now paves the way for correctly classifying similar enzymes from other organisms.
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Affiliation(s)
- Leonardo Astolfi Rosado
- From the Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), B-1050 Brussels, Belgium.,the Brussels Center for Redox Biology, B-1050 Brussels, Belgium.,Structural Biology Brussels and
| | - Khadija Wahni
- From the Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), B-1050 Brussels, Belgium.,the Brussels Center for Redox Biology, B-1050 Brussels, Belgium.,Structural Biology Brussels and
| | | | - Brandán Pedre
- From the Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), B-1050 Brussels, Belgium.,the Brussels Center for Redox Biology, B-1050 Brussels, Belgium.,Structural Biology Brussels and
| | - David Young
- From the Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), B-1050 Brussels, Belgium.,the Brussels Center for Redox Biology, B-1050 Brussels, Belgium.,Structural Biology Brussels and
| | - Alfonso G de la Rubia
- the Department of Molecular Biology, Area of Microbiology, University of León, 24071 León, Spain
| | | | - Edo Martens
- From the Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), B-1050 Brussels, Belgium.,the Brussels Center for Redox Biology, B-1050 Brussels, Belgium.,Structural Biology Brussels and
| | - Laura Marcos-Pascual
- the Department of Molecular Biology, Area of Microbiology, University of León, 24071 León, Spain
| | - Enea Sancho-Vaello
- the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain.,the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain
| | - David Albesa-Jové
- the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain.,the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain.,the Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain, and
| | | | - Charlotte Martin
- the Research Group of Organic Chemistry, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Vadim Makarov
- the A. N. Bakh Institute of Biochemistry, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Wim Versées
- From the Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), B-1050 Brussels, Belgium.,Structural Biology Brussels and
| | - Guido Verniest
- the Research Group of Organic Chemistry, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Marcelo E Guerin
- the Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas, Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain.,the Departamento de Bioquímica, Universidad del País Vasco, Leioa, Bizkaia 48940, Spain.,the Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain, and
| | - Luis M Mateos
- the Department of Molecular Biology, Area of Microbiology, University of León, 24071 León, Spain
| | | | - Joris Messens
- From the Center for Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), B-1050 Brussels, Belgium, .,the Brussels Center for Redox Biology, B-1050 Brussels, Belgium.,Structural Biology Brussels and
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4
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Netto LES, de Oliveira MA, Tairum CA, da Silva Neto JF. Conferring specificity in redox pathways by enzymatic thiol/disulfide exchange reactions. Free Radic Res 2016; 50:206-45. [DOI: 10.3109/10715762.2015.1120864] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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5
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Røhr ÅK, Hammerstad M, Andersson KK. Tuning of thioredoxin redox properties by intramolecular hydrogen bonds. PLoS One 2013; 8:e69411. [PMID: 23936007 PMCID: PMC3720550 DOI: 10.1371/journal.pone.0069411] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 06/07/2013] [Indexed: 01/22/2023] Open
Abstract
Thioredoxin-like proteins contain a characteristic C-x-x-C active site motif and are involved in a large number of biological processes ranging from electron transfer, cellular redox level maintenance, and regulation of cellular processes. The mechanism for deprotonation of the buried C-terminal active site cysteine in thioredoxin, necessary for dissociation of the mixed-disulfide intermediate that occurs under thiol/disulfide mediated electron transfer, is not well understood for all thioredoxin superfamily members. Here we have characterized a 8.7 kD thioredoxin (BC3987) from Bacillus cereus that unlike the typical thioredoxin appears to use the conserved Thr8 side chain near the unusual C-P-P-C active site to increase enzymatic activity by forming a hydrogen bond to the buried cysteine. Our hypothesis is based on biochemical assays and thiolate pKa titrations where the wild type and T8A mutant are compared, phylogenetic analysis of related thioredoxins, and QM/MM calculations with the BC3987 crystal structure as a precursor for modeling of reduced active sites. We suggest that our model applies to other thioredoxin subclasses with similar active site arrangements.
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6
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Heverly-Coulson GS, Boyd RJ, Mó O, Yáñez M. Revealing Unexpected Mechanisms for Nucleophilic Attack on SS and SeSe Bridges. Chemistry 2013; 19:3629-38. [DOI: 10.1002/chem.201203328] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 11/28/2012] [Indexed: 01/01/2023]
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7
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Takeda M, Terauchi T, Kainosho M. Conformational analysis by quantitative NOE measurements of the β-proton pairs across individual disulfide bonds in proteins. JOURNAL OF BIOMOLECULAR NMR 2012; 52:127-139. [PMID: 22131165 DOI: 10.1007/s10858-011-9587-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 11/08/2011] [Indexed: 05/31/2023]
Abstract
NOEs between the β-protons of cysteine residues across disulfide bonds in proteins provide direct information on the connectivities and conformations of these important cross-links, which are otherwise difficult to investigate. With conventional [U-(13)C, (15)N]-proteins, however, fast spin diffusion processes mediated by strong dipolar interactions between geminal β-protons prohibit the quantitative measurements and thus the analyses of long-range NOEs across disulfide bonds. We describe a robust approach for alleviating such difficulties, by using proteins selectively labeled with an equimolar mixture of (2R, 3S)-[β-(13)C; α,β-(2)H(2)] Cys and (2R, 3R)-[β-(13)C; α,β-(2)H(2)] Cys, but otherwise fully deuterated. Since either one of the prochiral methylene protons, namely β2 (proS) or β3 (proR), is always replaced with a deuteron and no other protons remain in proteins prepared by this labeling scheme, all four of the expected NOEs for the β-protons across disulfide bonds could be measured without any spin diffusion interference, even with long mixing times. Therefore, the NOEs for the β2 and β3 pairs across each of the disulfide bonds could be observed at high sensitivity, even though they are 25% of the theoretical maximum for each pair. With the NOE information, the disulfide bond connectivities can be unambiguously established for proteins with multiple disulfide bonds. In addition, the conformations around disulfide bonds, namely χ(2) and χ(3), can be determined based on the precise proton distances of the four β-proton pairs, by quantitative measurements of the NOEs across the disulfide bonds. The feasibility of this method is demonstrated for bovine pancreatic trypsin inhibitor, which has three disulfide bonds.
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Affiliation(s)
- Mitsuhiro Takeda
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
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8
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Cheng Z, Zhang J, Ballou DP, Williams CH. Reactivity of thioredoxin as a protein thiol-disulfide oxidoreductase. Chem Rev 2011; 111:5768-83. [PMID: 21793530 DOI: 10.1021/cr100006x] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Zhiyong Cheng
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-5606, USA
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9
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Webb H, Tynan-Connolly BM, Lee GM, Farrell D, O'Meara F, Søndergaard CR, Teilum K, Hewage C, McIntosh LP, Nielsen JE. Remeasuring HEWL pK(a) values by NMR spectroscopy: methods, analysis, accuracy, and implications for theoretical pK(a) calculations. Proteins 2010; 79:685-702. [PMID: 21287606 DOI: 10.1002/prot.22886] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 08/24/2010] [Accepted: 09/03/2010] [Indexed: 11/08/2022]
Abstract
Site-specific pK(a) values measured by NMR spectroscopy provide essential information on protein electrostatics, the pH-dependence of protein structure, dynamics and function, and constitute an important benchmark for protein pK(a) calculation algorithms. Titration curves can be measured by tracking the NMR chemical shifts of several reporter nuclei versus sample pH. However, careful analysis of these curves is needed to extract residue-specific pK(a) values since pH-dependent chemical shift changes can arise from many sources, including through-bond inductive effects, through-space electric field effects, and conformational changes. We have re-measured titration curves for all carboxylates and His 15 in Hen Egg White Lysozyme (HEWL) by recording the pH-dependent chemical shifts of all backbone amide nitrogens and protons, Asp/Glu side chain protons and carboxyl carbons, and imidazole protonated carbons and protons in this protein. We extracted pK(a) values from the resulting titration curves using standard fitting methods, and compared these values to each other, and with those measured previously by ¹H NMR (Bartik et al., Biophys J 1994;66:1180–1184). This analysis gives insights into the true accuracy associated with experimentally measured pK(a) values. We find that apparent pK(a) values frequently differ by 0.5–1.0 units depending upon the nuclei monitored, and that larger differences occasionally can be observed. The variation in measured pK(a) values, which reflects the difficulty in fitting and assigning pH-dependent chemical shifts to specific ionization equilibria, has significant implications for the experimental procedures used for measuring protein pK(a) values, for the benchmarking of protein pK(a) calculation algorithms, and for the understanding of protein electrostatics in general.
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Affiliation(s)
- Helen Webb
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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10
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Takeda M, Jee J, Terauchi T, Kainosho M. Detection of the Sulfhydryl Groups in Proteins with Slow Hydrogen Exchange Rates and Determination of Their Proton/Deuteron Fractionation Factors Using the Deuterium-Induced Effects on the 13Cβ NMR Signals. J Am Chem Soc 2010; 132:6254-60. [DOI: 10.1021/ja101205j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mitsuhiro Takeda
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan, and Center for Priority Areas, Graduate School of Science and Technology, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, 192-0397, Japan
| | - JunGoo Jee
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan, and Center for Priority Areas, Graduate School of Science and Technology, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, 192-0397, Japan
| | - Tsutomu Terauchi
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan, and Center for Priority Areas, Graduate School of Science and Technology, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, 192-0397, Japan
| | - Masatsune Kainosho
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan, and Center for Priority Areas, Graduate School of Science and Technology, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, 192-0397, Japan
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11
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Vitu E, Gross E, Greenblatt HM, Sevier CS, Kaiser CA, Fass D. Yeast Mpd1p Reveals the Structural Diversity of the Protein Disulfide Isomerase Family. J Mol Biol 2008; 384:631-40. [DOI: 10.1016/j.jmb.2008.09.052] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Revised: 09/02/2008] [Accepted: 09/16/2008] [Indexed: 02/06/2023]
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12
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Hernández G, Anderson JS, LeMaster DM. Electrostatic stabilization and general base catalysis in the active site of the human protein disulfide isomerase a domain monitored by hydrogen exchange. Chembiochem 2008; 9:768-78. [PMID: 18302150 DOI: 10.1002/cbic.200700465] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The nucleophilic Cys36 thiol of the human protein disulfide isomerase a domain is positioned over the N terminus of the alpha(2) helix. Amides in the active site exhibit diffusion-limited, hydroxide-catalyzed exchange, indicating that the local positive electrostatic potential decreases the pK value for peptide anion formation by at least 2 units so as to equal or exceed the acidity of water. In stark contrast to the pH dependence of exchange for simple peptides, the His38 amide in the reduced enzyme exhibits a maximum rate of exchange at pH 5 due to efficient general base catalysis by the neutral imidazole of its own side chain and suppression of its exchange by the ionization of the Cys36 thiol. Ionization of this thiol and deprotonation of the His38 side chain suppress the Cys39 amide hydroxide-catalyzed exchange by a million-fold. The electrostatic potential within the active site monitored by these exchange experiments provides a means of stabilizing the two distinct transition states that lead to substrate reduction and oxidation. Molecular modeling offers a role for the conserved Arg103 in coordinating the oxidative transition-state complex, thus providing further support for mechanisms of disulfide isomerization that utilize enzymatic catalysis at each step of the overall reaction.
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Affiliation(s)
- Griselda Hernández
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, School of Public Health, University at Albany-SUNY, Empire State Plaza, Albany, NY 12201, USA
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13
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Analyzing Protein NMR pH-Titration Curves. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s1574-1400(08)00005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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14
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Fass D. The Erv family of sulfhydryl oxidases. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2007; 1783:557-66. [PMID: 18155671 DOI: 10.1016/j.bbamcr.2007.11.009] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Revised: 11/18/2007] [Accepted: 11/20/2007] [Indexed: 10/22/2022]
Abstract
The Erv flavoenzymes contain a compact module that catalyzes the pairing of cysteine thiols into disulfide bonds. High-resolution structures of plant, animal, and fungal Erv enzymes that function in different contexts and intracellular compartments have been determined. Structural features can be correlated with biochemical properties, revealing how core sulfhydryl oxidase activity has been tailored to various functional niches. The introduction of disulfides into cysteine-containing substrates by Erv sulfhydryl oxidases is compared with the mechanisms used by NADPH-driven disulfide reductases and thioredoxin-like oxidoreductases to reduce and transfer disulfides, respectively.
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Affiliation(s)
- Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
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15
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Starks CM, Francois JA, MacArthur KM, Heard BZ, Kappock TJ. Atomic-resolution crystal structure of thioredoxin from the acidophilic bacterium Acetobacter aceti. Protein Sci 2007; 16:92-8. [PMID: 17192591 PMCID: PMC2222842 DOI: 10.1110/ps.062519707] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The crystal structure of thioredoxin (AaTrx) from the acetic acid bacterium Acetobacter aceti was determined at 1 A resolution. This is currently the highest resolution crystal structure available for any thioredoxin. Thioredoxins facilitate thiol-disulfide exchange, a process that is expected to be slow at the low pH values encountered in the A. aceti cytoplasm. Despite the apparent need to function at low pH, neither the active site nor the surface charge distribution of AaTrx is notably different from that of Escherichia coli thioredoxin. Apparently the ancestral thioredoxin was sufficiently stable for use in A. aceti or the need to interact with multiple targets constrained the variation of surface residues. The AaTrx structure presented here provides a clear view of all ionizable protein moieties and waters, a first step in understanding how thiol-disulfide exchange might occur in a low pH cytoplasm, and is a basis for biophysical studies of the mechanism of acid-mediated unfolding. The high resolution of this structure should be useful for computational studies of thioredoxin function, protein structure and dynamics, and side-chain ionization.
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Affiliation(s)
- Courtney M Starks
- Department of Chemistry, Washington University in Saint Louis, Missouri 63130, USA
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16
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Soler P, Bergès J, Fuster F, Chevreau H. Dynamical hydrogen-induced electronic relocalization in S2H2 and S2H2-. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2005.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Friemann R, Schmidt H, Ramaswamy S, Forstner M, Krauth-Siegel RL, Eklund H. Structure of thioredoxin from Trypanosoma brucei brucei. FEBS Lett 2003; 554:301-5. [PMID: 14623083 DOI: 10.1016/s0014-5793(03)01173-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The three-dimensional structure of thioredoxin from Trypanosoma brucei brucei has been determined at 1.4 A resolution. The overall structure is more similar to that of human thioredoxin than to any other thioredoxin structure. The most striking difference to other thioredoxins is the absence of a buried carboxylate behind the active site cysteines. Instead of the common Asp, there is a Trp that binds an ordered water molecule probably involved in the protonation/deprotonation of the more buried cysteine during catalysis. The conserved Trp in the WCGPC sequence motif has an exposed position that can interact with target proteins.
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Affiliation(s)
- Rosmarie Friemann
- Department of Molecular Biosciences, Swedish University of Agricultural Sciences, Biomedical Center, Box 590, S-75124 Uppsala, Sweden
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18
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Menchise V, Corbier C, Didierjean C, Saviano M, Benedetti E, Jacquot JP, Aubry A. Crystal structure of the wild-type and D30A mutant thioredoxin h of Chlamydomonas reinhardtii and implications for the catalytic mechanism. Biochem J 2001; 359:65-75. [PMID: 11563970 PMCID: PMC1222122 DOI: 10.1042/0264-6021:3590065] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Thioredoxins are ubiquitous proteins which catalyse the reduction of disulphide bridges on target proteins. The catalytic mechanism proceeds via a mixed disulphide intermediate whose breakdown should be enhanced by the involvement of a conserved buried residue, Asp-30, as a base catalyst towards residue Cys-39. We report here the crystal structure of wild-type and D30A mutant thioredoxin h from Chlamydomonas reinhardtii, which constitutes the first crystal structure of a cytosolic thioredoxin isolated from a eukaryotic plant organism. The role of residue Asp-30 in catalysis has been revisited since the distance between the carboxylate OD1 of Asp-30 and the sulphur SG of Cys-39 is too great to support the hypothesis of direct proton transfer. A careful analysis of all available crystal structures reveals that the relative positioning of residues Asp-30 and Cys-39 as well as hydrophobic contacts in the vicinity of residue Asp-30 do not allow a conformational change sufficient to bring the two residues close enough for a direct proton transfer. This suggests that protonation/deprotonation of Cys-39 should be mediated by a water molecule. Molecular-dynamics simulations, carried out either in vacuo or in water, as well as proton-inventory experiments, support this hypothesis. The results are discussed with respect to biochemical and structural data.
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Affiliation(s)
- V Menchise
- Laboratoire de Cristallographie et Modélisation des Matériaux Minéraux et Biologiques, Groupe Biocristallographie, ESA 7036, Université Henri Poincaré-Nancy I, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France
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Capitani G, Marković-Housley Z, DelVal G, Morris M, Jansonius JN, Schürmann P. Crystal structures of two functionally different thioredoxins in spinach chloroplasts. J Mol Biol 2000; 302:135-54. [PMID: 10964566 DOI: 10.1006/jmbi.2000.4006] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Thioredoxins are small ubiquitous proteins which act as general protein disulfide reductases in living cells. Chloroplasts contain two distinct thioredoxins ( f and m) with different phylogenetic origin. Both act as enzyme regulatory proteins but have different specificities towards target enzymes. Thioredoxin f (Trx f), which shares only low sequence identity with thioredoxin m (Trx m) and with all other known thioredoxins, activates enzymes of the Calvin cycle and other photosynthetic processes. Trx m shows high sequence similarity with bacterial thioredoxins and activates other chloroplast enzymes. The here described structural studies of the two chloroplast thioredoxins were carried out in order to gain insight into the structure/function relationships of these proteins. Crystal structures were determined for oxidized, recombinant thioredoxin f (Trx f-L) and at the N terminus truncated form of it (Trx f-S), as well as for oxidized and reduced thioredoxin m (at 2.1 and 2.3 A resolution, respectively). Whereas thioredoxin f crystallized as a monomer, both truncated thioredoxin f and thioredoxin m crystallized as non-covalent dimers. The structures of thioredoxins f and m exhibit the typical thioredoxin fold consisting of a central twisted five-stranded beta-sheet surrounded by four alpha-helices. Thioredoxin f contains an additional alpha-helix at the N terminus and an exposed third cysteine close to the active site. The overall three-dimensional structures of the two chloroplast thioredoxins are quite similar. However, the two proteins have a significantly different surface topology and charge distribution around the active site. An interesting feature which might significantly contribute to the specificity of thioredoxin f is an inherent flexibility of its active site, which has expressed itself crystallographically in two different crystal forms.
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Affiliation(s)
- G Capitani
- Structural Biology Division Biozentrum, University of Basel, Basel, CH-4056, Switzerland.
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20
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Mössner E, Iwai H, Glockshuber R. Influence of the pK(a) value of the buried, active-site cysteine on the redox properties of thioredoxin-like oxidoreductases. FEBS Lett 2000; 477:21-6. [PMID: 10899304 DOI: 10.1016/s0014-5793(00)01738-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thioredoxin constitutes the prototype of the thiol-disulfide oxidoreductase family. These enzymes contain an active-site disulfide bridge with the consensus sequence Cys-Xaa-Xaa-Cys. The more N-terminal active-site cysteine is generally a strong nucleophile with an abnormal low pK(a) value. In contrast, the more C-terminal cysteine is buried and only little is known about its effective pK(a) during catalysis of disulfide exchange reactions. Here we have analyzed the pK(a) values of the active-site thiols in wild type thioredoxin and a 400-fold more oxidizing thioredoxin variant by NMR spectroscopy, using selectively (13)C(beta)-Cys-labeled proteins. We find that the effective pK(a) of the buried cysteine (pK(b)) of the variant is increased, while the pK(a) of the more N-terminal cysteine (pK(N)) is decreased relative to the corresponding pK(a) values in the wild type. We propose two empirical models which exclusively require the knowledge of pK(N) to predict the redox properties of thiol-disulfide oxidoreductases with reasonable accuracy.
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Affiliation(s)
- E Mössner
- Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Hönggerberg, CH-8093, Zürich, Switzerland
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21
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Vohník S, Hanson C, Tuma R, Fuchs JA, Woodward C, Thomas GJ. Conformation, stability, and active-site cysteine titrations of Escherichia coli D26A thioredoxin probed by Raman spectroscopy. Protein Sci 1998; 7:193-200. [PMID: 9514274 PMCID: PMC2143819 DOI: 10.1002/pro.5560070120] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The active-site cysteines (Cys 32 and Cys 35) of Escherichia coli thioredoxin are oxidized to a disulfide bridge when the protein mediates substrate reduction. In reduced thioredoxin, Cys 32 and Cys 35 are characterized by abnormally low pKa values. A conserved side chain, Asp 26, which is sterically accessible to the active site, is also essential to oxidoreductase activity. pKa values governing cysteine thiol-thiolate equilibria in the mutant thioredoxin, D26A, have been determined by direct Raman spectrophotometric measurement of sulfhydryl ionizations. The results indicate that, in D26A thioredoxin, both sulfhydryls titrate with apparent pKa values of 7.5+/-0.2, close to values measured previously for wild-type thioredoxin. Sulfhydryl Raman markers of D26A and wild-type thioredoxin also exhibit similar band shapes, consistent with minimal differences in respective cysteine side-chain conformations and sulfhydryl interactions. The results imply that neither the Cys 32 nor Cys 35 SH donor is hydrogen bonded directly to Asp 26 in the wild-type protein. Additionally, the thioredoxin main-chain conformation is largely conserved with D26A mutation. Conversely, the mutation perturbs Raman bands diagnostic of tryptophan (Trp 28 and Trp 31) orientations and leads to differences in their pH dependencies, implying local conformational differences near the active site. We conclude that, although the carboxyl side chain of Asp 26 neither interacts directly with active-site cysteines nor is responsible for their abnormally low pKa values, the aspartate side chain may play a role in determining the conformation of the enzyme active site.
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Affiliation(s)
- S Vohník
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, 64110, USA
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LeMaster DM, Springer PA, Unkefer CJ. The role of the buried aspartate of Escherichia coli thioredoxin in the activation of the mixed disulfide intermediate. J Biol Chem 1997; 272:29998-30001. [PMID: 9374473 DOI: 10.1074/jbc.272.48.29998] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The structurally homologous protein disulfide isomerases and thioredoxins exhibit a 10(5) variation of redox equilibria. It is demonstrated that the kinetic distinction among these protein family members lies primarily in the rate of breakdown of the mixed disulfide intermediate. The conserved buried acid group serves as a proton transfer catalyst for the buried active site cysteine in the formation and breakdown of the mixed disulfide. The reduction rate of Escherichia coli thioredoxin by dithiothreitol is directly proportional to the fraction of Asp-26 in the protonated form over the pH range of 6-9. The kinetic role of Asp-26 is further probed via differential solvent kinetic isotope effect measurements versus a D26N variant. The differential solvent isotope effect of 0.6 is consistent with a direct proton donation to the thiolate leaving group (Cys-35) via an enforced general acid catalysis by trapping mechanism. Such a donation necessitates a structural rearrangement as these two buried side chains are separated by 6 A in both the oxidized and reduced forms of the protein.
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Affiliation(s)
- D M LeMaster
- Chemical Science and Technology Group 4, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.
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Bunik V, Follmann H, Bisswanger H. Activation of mitochondrial 2-oxoacid dehydrogenases by thioredoxin. Biol Chem 1997; 378:1125-30. [PMID: 9372181 DOI: 10.1515/bchm.1997.378.10.1125] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The regulation of mitochondrial dehydrogenases of 2-oxoacids by thioredoxin is established. It is found that at low NAD+ and saturating concentrations of 2-oxoacids and CoA, inactivation of 2-oxoacid dehydrogenase complexes takes place, preventing NAD+ reduction under such conditions. However, addition of oxidized E. coli thioredoxin to the reaction medium without dithiothreitol allows effective NAD+ reduction at this substrate ratio. Product accumulation curves show that thioredoxin activates the complexes by protecting them from the inactivation observed in the conditions when the complex-bound dihydrolipoate is accumulated. Disappearance of the activatory effect of thioredoxin after its treatment with SH-specific reagents indicates the involvement of the redox-active cysteine couple of thioredoxin in its activation of 2-oxoacid dehydrogenase complexes. The redox-inactive thioredoxin not only shows no activation, but in fact exerts an inhibitory effect. The inhibition manifests the complex formation between SH-modified thioredoxin and dehydrogenase systems, involving amino acid residues of thioredoxin other than cysteine. High efficiency of thioredoxin from E. coli as compared to chloroplast thioredoxin f and glutathione disulfide is revealed. This indicates the importance of specific protein structure also for the influence of the redox-active thioredoxin upon the 2-oxoacid dehydrogenase complexes. The results obtained suggest that these key enzyme systems of mitochondrial metabolism represent previously unidentified targets for the action of mitochondrial thioredoxin, which is known to resemble the E. coli counterpart studies in this work.
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Affiliation(s)
- V Bunik
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Russia
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