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Tcherkez G. The mechanism of Rubisco-catalysed oxygenation. PLANT, CELL & ENVIRONMENT 2016; 39:983-997. [PMID: 26286702 DOI: 10.1111/pce.12629] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/28/2015] [Accepted: 08/09/2015] [Indexed: 06/04/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the cornerstone of photosynthetic carbon assimilation because it catalyses the fixation of CO2 onto ribulose-1,5-bisphosphate (RuBP). The enzyme also catalyses RuBP oxygenation, thereby evolving phosphoglycolate which is recycled along the photorespiratory pathway. Oxygenation is quantitatively important, because under ordinary gaseous conditions, more than one third of RuBP molecules are oxygenated rather than carboxylated. However, contrary to carboxylation, the chemical mechanism of oxygenation is not well known, and little progress has been made since the early 80s. Here, I review recent experimental data that provide some new insights into the reaction mechanism, and carry out simple calculations of kinetic parameters. Isotope effects suggest that oxygenation is less likely initiated by a redox phenomenon (such as superoxide production) and more likely involves concerted chemical events that imply interactions with protons. A possible energy profile of the reaction is drawn which suggests that the generation of the oxygenated reaction intermediate (peroxide) is irreversible. Possible changes in oxygenation-associated rate constants between Rubisco forms are discussed.
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Affiliation(s)
- Guillaume Tcherkez
- Research School of Biology, ANU College of Medicine, Biology and Environment, Australian National University, Canberra, 2601, ACT, Australia
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2
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Bunik VI, Schloss JV, Pinto JT, Dudareva N, Cooper AJL. A survey of oxidative paracatalytic reactions catalyzed by enzymes that generate carbanionic intermediates: implications for ROS production, cancer etiology, and neurodegenerative diseases. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2011; 77:307-60. [PMID: 21692372 DOI: 10.1002/9780470920541.ch7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Victoria I Bunik
- School of Bioinformatics and Bioengineering, and Belozersky Institute of Physico-Chemical Biology, Moscow Lomonosov State University, Moscow, Russian Federation
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Lee DS, Flachsová E, Bodnárová M, Demeler B, Martásek P, Raman CS. Structural basis of hereditary coproporphyria. Proc Natl Acad Sci U S A 2005; 102:14232-7. [PMID: 16176984 PMCID: PMC1224704 DOI: 10.1073/pnas.0506557102] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2004] [Indexed: 11/18/2022] Open
Abstract
Hereditary coproporphyria is an autosomal dominant disorder resulting from the half-normal activity of coproporphyrinogen oxidase (CPO), a mitochondrial enzyme catalyzing the antepenultimate step in heme biosynthesis. The mechanism by which CPO catalyzes oxidative decarboxylation, in an extraordinary metal- and cofactor-independent manner, is poorly understood. Here, we report the crystal structure of human CPO at 1.58-A resolution. The structure reveals a previously uncharacterized tertiary topology comprising an unusually flat seven-stranded beta-sheet sandwiched by alpha-helices. In the biologically active dimer (K(D) = 5 x 10(-7) M), one monomer rotates relative to the second by approximately 40 degrees to create an intersubunit interface in close proximity to two independent enzymatic sites. The unexpected finding of citrate at the active site allows us to assign Ser-244, His-258, Asn-260, Arg-262, Asp-282, and Arg-332 as residues mediating substrate recognition and decarboxylation. We favor a mechanism in which oxygen serves as the immediate electron acceptor, and a substrate radical or a carbanion with substantial radical character participates in catalysis. Although several mutations in the CPO gene have been described, the molecular basis for how these alterations diminish enzyme activity is unknown. We show that deletion of residues (392-418) encoded by exon six disrupts dimerization. Conversely, harderoporphyria-causing K404E mutation precludes a type I beta-turn from retaining the substrate for the second decarboxylation cycle. Together, these findings resolve several questions regarding CPO catalysis and provide insights into hereditary coproporphyria.
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Affiliation(s)
- Dong-Sun Lee
- Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, TX 77030, USA
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4
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Structural framework for catalysis and regulation in ribulose-1,5-bisphosphate carboxylase/oxygenase. Arch Biochem Biophys 2003; 414:130-40. [PMID: 12781764 DOI: 10.1016/s0003-9861(03)00164-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the enzyme assimilating CO2 in biology. Despite serious efforts, using many different methods, a detailed understanding of activity and regulation in Rubisco still eludes us. New results in X-ray crystallography may provide a structural framework on which to base experimental approaches for more detailed analyses of the function of Rubisco at the molecular level. This article gives a critical review of the field and summarizes recent results from structural studies of Rubisco.
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Oliva M, Safont VS, Andrés J, Tapia O. Transition Structures for d-Ribulose-1,5-bisphosphate Carboxylase/Oxygenase-Catalyzed Oxygenation Chemistry: Role of Carbamylated Lysine in a Model Magnesium Coordination Sphere. J Phys Chem A 2001. [DOI: 10.1021/jp004287y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mónica Oliva
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
| | - Vicent S. Safont
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
| | - Juan Andrés
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
| | - O. Tapia
- Department of Physical Chemistry, Uppsala University, Box 532, S-75121 Uppsala, Sweden
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6
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Aguado A. Ga+, In+, and Tl+ impurities in alkali halide crystals: Distortion trends. J Chem Phys 2000. [DOI: 10.1063/1.1317520] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Tapia O, Oliva M, Safont VS, Andrés J. A quantum-chemical study of transition structures for enolization and oxygenation steps catalyzed by rubisco: on the role of magnesium and carbamylated Lys-201 in opening oxygen capture channel. Chem Phys Lett 2000. [DOI: 10.1016/s0009-2614(00)00500-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Oliva M, Safont VS, Andrés J, Tapia O. A Theoretical Study of the Molecular Mechanism for the Carboxylation Chemistry in Rubisco. J Phys Chem A 1999. [DOI: 10.1021/jp992052k] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. Oliva
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
| | - V. S. Safont
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
| | - J. Andrés
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain
| | - O. Tapia
- Department of Physical Chemistry, Uppsala University, Box 532,S-75121 Uppsala, Sweden
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10
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Oliva M, Safont VS, Andrés J, Tapia O. Theoretical Study of the Molecular Mechanism for the Oxygenation Chemistry in Rubisco. J Phys Chem A 1999. [DOI: 10.1021/jp9907342] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Oliva
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain, and Department of Physical Chemistry, Uppsala University, Box 532, S-85121 Uppsala, Sweden
| | - V. S. Safont
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain, and Department of Physical Chemistry, Uppsala University, Box 532, S-85121 Uppsala, Sweden
| | - J. Andrés
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain, and Department of Physical Chemistry, Uppsala University, Box 532, S-85121 Uppsala, Sweden
| | - O. Tapia
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain, and Department of Physical Chemistry, Uppsala University, Box 532, S-85121 Uppsala, Sweden
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Cleland WW, Andrews TJ, Gutteridge S, Hartman FC, Lorimer GH. Mechanism of Rubisco: The Carbamate as General Base. Chem Rev 1998; 98:549-562. [PMID: 11848907 DOI: 10.1021/cr970010r] [Citation(s) in RCA: 279] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- W. Wallace Cleland
- The Institute for Enzyme Research, University of Wisconsin, Madison, Wisconsin 53705, Research School of Biological Sciences, Australian National University, Canberra 2601, Australia, Central Research and Development Department, Dupont Company, Experimental Station, Wilmington, Delaware 19880-0402, and Protein Engineering Program, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-8077
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13
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Tapia O, Andrés J, Safont V. Transition structures in vacuo and the theory of enzyme catalysis. Rubisco's catalytic mechanism: a paradigmatic case? ACTA ACUST UNITED AC 1995. [DOI: 10.1016/0166-1280(95)90101-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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14
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Harpel MR, Serpersu EH, Lamerdin JA, Huang ZH, Gage DA, Hartman FC. Oxygenation mechanism of ribulose-bisphosphate carboxylase/oxygenase. Structure and origin of 2-carboxytetritol 1,4-bisphosphate, a novel O2-dependent side product generated by a site-directed mutant. Biochemistry 1995; 34:11296-306. [PMID: 7669788 DOI: 10.1021/bi00035a039] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Site-directed mutagenesis has implicated active-site Lys329 of Rhodospirillum rubrum ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in promoting the reaction of CO2 with the 2,3-enediol of ribulose bisphosphate and in stabilizing carboxylation intermediates [Hartman, F. C., & Lee, E. H. (1989) J. Biol. Chem. 264, 11784-11789; Lorimer, G. H., Chen, Y.-R., & Hartman, F. C. (1993) Biochemistry 32, 9018-9024]. Although the K329A mutant is greatly impaired in carboxylation, it catalyzes formation of the enediol, which is misprocessed to an O2-dependent side product [Harpel, M. R., & Hartman, F. C. (1994) Biochemistry 33, 5553-5561]. We now identify this novel side product as 2-carboxytetritol 1,4-bisphosphate (CTBP) by mass spectrometry, 1H-, 13C-, and 31P-NMR spectroscopy, and periodate oxidation. H2O2 accumulates during formation of CTBP, which we show to be derived from a transient precursor, the dicarbonyl D-glycero-2,3-pentodiulose 1,5-bisphosphate. The isolated dicarbonyl bisphosphate is processed by K329A to CTBP. These results, combined with isotope-labeling studies, suggest that CTBP arises by H2O2 elimination from an improperly stabilized peroxy adduct of the enediol intermediate, followed by rearrangement of the resulting dicarbonyl. Therefore, normal oxygenation, as catalyzed by wild-type Rubisco, is not a spontaneous reaction but must involve stabilization of the peroxy intermediate to mitigate formation of the dicarbonyl bisphosphate and subsequently CTBP. CTBP formation verifies the identity of Rubisco's previously invoked oxygenase intermediate, provides additional mechanistic insight into the oxygenation reaction, and shows that Lys329 promotes oxygenation as well as carboxylation. These results may be relevant to other oxygenases, which also exploit substrate carbanions rather than organic cofactors or transition metals for biological oxygen utilization.
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Affiliation(s)
- M R Harpel
- Protein Engineering Program, Oak Ridge National Laboratory, Tennessee 37831, USA
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Harpel MR, Hartman FC. Chemical rescue by exogenous amines of a site-directed mutant of ribulose 1,5-bisphosphate carboxylase/oxygenase that lacks a key lysyl residue. Biochemistry 1994; 33:5553-61. [PMID: 8180178 DOI: 10.1021/bi00184a026] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Ligand binding to ribulose 1,5-bisphosphate carboxylase/oxygenase immobilizes the flexible loop 6 of the beta/alpha barrel domain in its closed conformation. Lys329, located at the apex of this loop, interacts electrostatically with Glu48 of the adjacent subunit and with the CO2-derived carboxylate of the carboxylated reaction intermediate [Knight et al. (1990) J. Mol. Biol. 215, 113-160]. Previous studies have implicated Lys329 in the addition of CO2 to the initial enediol(ate) intermediate: mutants at position 329 catalyze enolization of ribulose 1,5-bisphosphate and processing of isolated carboxyketone intermediate, but are severely impaired in overall carboxylation and the tight-binding of the carboxylated intermediate analogue 2-carboxyarabinitol 1,5-bisphosphate. Using the chemical rescue method of Toney and Kirsch [(1989) Science 243, 1485-1488], we show that these defects are partially overcome by exogenous amines. For example, ethylamine enhances the carboxylation rate of K329A by about 80-fold and strengthens complexation of 2-carboxyarabinitol 1,5-bisphosphate. The CO2/O2 specificity of K329A is increased by amines, but remains lower than the wild-type value. Despite the pronounced enhancement of carboxylase activity, amines do not influence the rate at which ribulose 1,5-bisphosphate is enolized by K329A. Rescue of K329A follows an apparent Brønsted relationship with a beta of 1, implying complete protonation of amine in the rescued transition state. Rate saturation with respect to amine concentration and the different steric preferences for amines between K329A and K329C suggest that the amines bind to the enzyme in the position voided by the mutation.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- M R Harpel
- Protein Engineering Program, Oak Ridge National Laboratory, Tennessee 37831-8077
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16
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Computer assisted simulations and molecular graphics methods in molecular design. 1. Theory and applications to enzyme active-site directed drug design. ACTA ACUST UNITED AC 1994. [DOI: 10.1007/bf01003761] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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Tapia O, Andrés J, Safont VS. Enzyme catalysis and transition structures in vacuo. Transition structures for the enolization, carboxylation and oxygenation reactions in ribulose-1,5-bisphosphate carboxylase/oxygenase enzyme (Rubisco). ACTA ACUST UNITED AC 1994. [DOI: 10.1039/ft9949002365] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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