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Shen X, Sun T, Dai M, Aslam MMA, Peng C. Performance and mechanistic study of biochar and magnesium-enhanced phytoremediation in cadmium-contaminated soil by alfalfa. CHEMOSPHERE 2024; 362:142737. [PMID: 38950747 DOI: 10.1016/j.chemosphere.2024.142737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024]
Abstract
Recently, phytoremediation has been regarded as a green and environment friendly technique to treat metals contaminated soils. Thus, in this study, pot experiments were designed to investigate the combine effects of biochar and magnesium (MPs) to purify cadmium (Cd)-contaminated soils by Medicago sativa L. (alfalfa). The results showed that the combined use of biochar and Mg significantly increased the accumulation of Cd and promoted the transport of Cd from root to shoot in alfalfa, simultaneously. Importantly, the combined use of biochar and Mg could increase the accumulation of Cd in shoot and whole plant (shoot + root) of alfalfa up-to 59.1% and 23.1%, respectively. Moreover, the enhancement mechanism can be analyzed from several aspects. Firstly, the photosynthesis was enhanced, which was beneficial to plant growth. The product of photosynthesis provided energy for uptake and transport of Cd. Meanwhile, its transport in phloem could promote the transport of Cd. Secondly, the enhancement of antioxidant capacity of alfalfa effectively protected the membrane structure of alfalfa, which indicated that Cd could enter alfalfa from the channel on the cell membrane. Lastly, the chemical form of Cd and microbial community structure in soil were changed. Overall, these changes reduced the Cd toxicity in soil, enhanced the resistance capability of alfalfa, increased the Cd uptake by alfalfa and promoted the growth of alfalfa. Thus, the obtained results suggested that the combined use of biochar and Mg is an effective approach to enhance phytoremediation performance for purifying Cd-contaminated soils.
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Affiliation(s)
- Xing Shen
- School of Chemical and Environmental Engineering, Anhui Polytechnic University, Wuhu, 241000, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Taotao Sun
- School of Chemical and Environmental Engineering, Anhui Polytechnic University, Wuhu, 241000, China; Observation and Research Station of Seawater Intrusion and Soil Salinization, Laizhou Bay, Ministry of Natural Resources, Qingdao, Shandong Province, 266061, China
| | - Min Dai
- Guangdong Provincial Key Laboratory of Environmental Health and Land Resource, Zhaoqing University, Zhaoqing, 526061, China
| | - Mian M Ahson Aslam
- School of Chemical and Environmental Engineering, Anhui Polytechnic University, Wuhu, 241000, China; Observation and Research Station of Seawater Intrusion and Soil Salinization, Laizhou Bay, Ministry of Natural Resources, Qingdao, Shandong Province, 266061, China
| | - Changsheng Peng
- School of Chemical and Environmental Engineering, Anhui Polytechnic University, Wuhu, 241000, China; Guangdong Provincial Key Laboratory of Environmental Health and Land Resource, Zhaoqing University, Zhaoqing, 526061, China.
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2
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Bjelčić M, Aurelius O, Nan J, Neutze R, Ursby T. Room-temperature serial synchrotron crystallography structure of Spinacia oleracea RuBisCO. Acta Crystallogr F Struct Biol Commun 2024; 80:117-124. [PMID: 38809540 PMCID: PMC11189101 DOI: 10.1107/s2053230x24004643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/18/2024] [Indexed: 05/30/2024] Open
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the enzyme responsible for the first step of carbon dioxide (CO2) fixation in plants, which proceeds via the carboxylation of ribulose 1,5-biphosphate. Because of the enormous importance of this reaction in agriculture and the environment, there is considerable interest in the mechanism of fixation of CO2 by RuBisCO. Here, a serial synchrotron crystallography structure of spinach RuBisCO is reported at 2.3 Å resolution. This structure is consistent with earlier single-crystal X-ray structures of this enzyme and the results are a good starting point for a further push towards time-resolved serial synchrotron crystallography in order to better understand the mechanism of the reaction.
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Affiliation(s)
- Monika Bjelčić
- MAX IV Laboratory, Lund UniversityPO Box 118221 00LundSweden
| | - Oskar Aurelius
- MAX IV Laboratory, Lund UniversityPO Box 118221 00LundSweden
| | - Jie Nan
- MAX IV Laboratory, Lund UniversityPO Box 118221 00LundSweden
| | - Richard Neutze
- Department of Chemistry and Molecular BiologyUniversity of GothenburgMedicinaregatan 9C413 90GothenburgSweden
| | - Thomas Ursby
- MAX IV Laboratory, Lund UniversityPO Box 118221 00LundSweden
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3
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Huang Q, Szebenyi DME. Crystal structure of a type III Rubisco in complex with its product 3-phosphoglycerate. Proteins 2023; 91:330-337. [PMID: 36151846 DOI: 10.1002/prot.26431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 02/04/2023]
Abstract
The crystal structure of the complex of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco; EC 4.1.1.39) from Archaeoglobus fulgidus (afRubisco) with its products 3PGAs has been determined to a resolution of 1.7 Å and is of the closed form. Type III Rubiscos such as afRubisco have 18 out of the 19 essential amino acid residues of canonical Rubisco; the 19th is Tyr rather than Phe. Superposition with the structure of a complex of the similar tkRubisco with the six-carbon intermediate analog 2CABP shows the same conformation of the 19 residues except for Glu46 and Thr51. Glu46 adopts a unique conformation different from that in other Rubiscos and makes two H-bonds with the ligand 3PGA. Similar to other closed state Rubiscos, the backbone of Thr51 is rotated and the side chain makes an H-bond with the ligand 3PGA. Two product 3PGA molecules are bound at the active site, overlapping well with the 2CABP of tkRubisco/2CABP. The positions of the P1 and P2 phosphate groups differ by 0.4 and 0.53 Å, respectively, between 2CABP and the two 3PGAs. This afRubisco/3PGA complex mimics an intermediate stage of the carboxylation reaction which occurs after the production of the two 3PGA products but before the reopening of the active site. The stability of this complex suggests that the Rubisco active site will not reopen before both 3PGA products are formed.
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Affiliation(s)
- Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, New York, USA
| | - Doletha M E Szebenyi
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, New York, USA
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4
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Kim H, Park J, Lim S, Jun SH, Jung M, Roh SH. Cryo-EM structures of GroEL:ES 2 with RuBisCO visualize molecular contacts of encapsulated substrates in a double-cage chaperonin. iScience 2022; 25:103704. [PMID: 35036883 PMCID: PMC8749442 DOI: 10.1016/j.isci.2021.103704] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/12/2021] [Accepted: 12/23/2021] [Indexed: 10/24/2022] Open
Abstract
The GroEL/GroES chaperonin system assists the folding of many proteins, through conformational transitions driven by ATP hydrolysis. Although structural information about bullet-shaped GroEL:ES1 complexes has been extensively reported, the substrate interactions of another functional complex, the football-shaped GroEL:ES2, remain elusive. Here, we report single-particle cryo-EM structures of reconstituted wild-type GroEL:ES2 complexes with a chemically denatured substrate, ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO). Our structures demonstrate that native-like folded RuBisCO density is captured at the lower part of the GroEL chamber and that GroEL's bulky hydrophobic residues Phe281, Tyr360, and Phe44 contribute to direct contact with RuBisCO density. In addition, our analysis found that GroEL:ES2 can be occupied by two substrates simultaneously, one in each chamber. Together, these observations provide insights to the football-shaped GroEL:ES2 complex as a functional state to assist the substrate folding with visualization.
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Affiliation(s)
- Hyunmin Kim
- School of Biology, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Junsun Park
- School of Biology, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Seyeon Lim
- School of Biology, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung-Hoon Jun
- Korea Basic Science Institute, Ochang 28119, Republic of Korea
| | - Mingyu Jung
- School of Biology, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Soung-Hun Roh
- School of Biology, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
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Yang Y, Li X, Kan B, He H, Li T, Ding Y, Du P, Lai W, Hu H, Huang J. Transcriptome analysis reveals MYB and WRKY transcription factors involved in banana (Musa paradisiaca AA) magnesium deficiency. PLANTA 2021; 254:115. [PMID: 34743252 DOI: 10.1007/s00425-021-03769-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
The banana development was inhibited under the long-term magnesium deficiency (MD) stress, resulting in the leaf chlorosis. MYB108 and WRKY75 are involved in regulating the growth and development of banana leaves and roots under long-term MD. Magnesium deficiency (MD) causes plant growth inhibition, ageing acceleration, yield reduction and quality decline of banana (Musa paradisiaca AA), but the molecular regulatory mechanisms underlying the changes in response to long-term MD conditions remain unknown. In this study, a long-term MD experiment was performed with banana seedlings at the four-leaf stage. Compared to those in the control group, the growth of leaves and roots of seedlings in the long-term MD treatment experimental groups was inhibited, and the Mg content and chlorophyll contents were decreased. Leaves and roots of seedlings from the control and experimental groups were subsequently collected for RNA sequencing to identify the genes that respond to long-term MD. More than 50 million reads were identified from each sample, resulting in the detection of 3500 and 948 differentially expressed genes (DEGs) in the leaves and roots, respectively. MYB and WRKY transcription factors (TFs) involved in plant stress responses were selected for further analysis, and 102 MYB and 149 WRKY TFs were differentially expressed. Furthermore, two highly differentially expressed candidate genes, MYB108 and WRKY75, were functionally analyzed using Arabidopsis mutants grown under long-term MD conditions. The results showed that the density of root hairs on the wild type (WT) was than that on the myb108 and wrky75 mutants under MD, implying that the mutants were more sensitive to MD than the WT. This research broadens our understanding the underlying molecular mechanism of banana seedlings adapted to the long-term MD condition.
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Affiliation(s)
- Yong Yang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Xinping Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Baolin Kan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Hongsu He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Ting Li
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Yuanhao Ding
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Pengmeng Du
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Wenjie Lai
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Haiyan Hu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, School of Tropical Crops, Hainan University, Haikou, 570228, China.
| | - Jiaquan Huang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, School of Tropical Crops, Hainan University, Haikou, 570228, China.
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6
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Tian XY, He DD, Bai S, Zeng WZ, Wang Z, Wang M, Wu LQ, Chen ZC. Physiological and molecular advances in magnesium nutrition of plants. PLANT AND SOIL 2021; 468:1-17. [PMID: 0 DOI: 10.1007/s11104-021-05139-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/25/2021] [Indexed: 05/27/2023]
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7
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The Mechanism of Rubisco Catalyzed Carboxylation Reaction: Chemical Aspects Involving Acid-Base Chemistry and Functioning of the Molecular Machine. Catalysts 2021. [DOI: 10.3390/catal11070813] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In recent years, a great deal of attention has been paid by the scientific community to improving the efficiency of photosynthetic carbon assimilation, plant growth and biomass production in order to achieve a higher crop productivity. Therefore, the primary carboxylase enzyme of the photosynthetic process Rubisco has received considerable attention focused on many aspects of the enzyme function including protein structure, protein engineering and assembly, enzyme activation and kinetics. Based on its fundamental role in carbon assimilation Rubisco is also targeted by the CO2-fertilization effect, which is the increased rate of photosynthesis due to increasing atmospheric CO2-concentration. The aim of this review is to provide a framework, as complete as possible, of the mechanism of the RuBP carboxylation/hydration reaction including description of chemical events occurring at the enzyme “activating” and “catalytic” sites (which involve Broensted acid-base reactions) and the functioning of the complex molecular machine. Important research results achieved over the last few years providing substantial advancement in understanding the enzyme functioning will be discussed.
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8
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Park H, Park K, Kim N, Kim N, Jeong SK, Yoon S. A
CO
2
Absorbent Articulated by Imitating the
RuBisCO
Regulation Site. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.12180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Hongjin Park
- Department of Chemistry Chung‐Ang University Dongjak‐gu,Seoul Republic of Korea
| | - Kwangho Park
- Clean Energy Research Centre Korea Institute of Science and Technology Chengryang, Seoul Republic of Korea
| | - Namseok Kim
- Department of Chemistry Chung‐Ang University Dongjak‐gu,Seoul Republic of Korea
| | - Nak‐Kyoon Kim
- Advanced Analysis Center, Korea Institute of Science and Technology Seongbuk‐gu, Seoul 136791 Republic of Korea
| | - Soon Kwan Jeong
- Korea Institute of Energy Research Daejeon Republic of Korea
| | - Sungho Yoon
- Department of Chemistry Chung‐Ang University Dongjak‐gu,Seoul Republic of Korea
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9
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Reaction of ribulose biphosphate carboxylase/oxygenase assembled on a DNA scaffold. Bioorg Med Chem 2019; 27:115120. [DOI: 10.1016/j.bmc.2019.115120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/10/2019] [Accepted: 09/12/2019] [Indexed: 12/30/2022]
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10
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Satagopan S, North JA, Arbing MA, Varaljay VA, Haines SN, Wildenthal JA, Byerly KM, Shin A, Tabita FR. Structural Perturbations of Rhodopseudomonas palustris Form II RuBisCO Mutant Enzymes That Affect CO2 Fixation. Biochemistry 2019; 58:3880-3892. [DOI: 10.1021/acs.biochem.9b00617] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Sriram Satagopan
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Justin A. North
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mark A. Arbing
- UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Vanessa A. Varaljay
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sidney N. Haines
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - John A. Wildenthal
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kathryn M. Byerly
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Annie Shin
- UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - F. Robert Tabita
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
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11
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The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism. Microbiol Mol Biol Rev 2018; 83:83/1/e00040-18. [PMID: 30567937 DOI: 10.1128/mmbr.00040-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ribosyl 1,5-bisphosphate (PRibP) was discovered 65 years ago and was believed to be an important intermediate in ribonucleotide metabolism, a role immediately taken over by its "big brother" phosphoribosyldiphosphate. Only recently has PRibP come back into focus as an important player in the metabolism of ribonucleotides with the discovery of the pentose bisphosphate pathway that comprises, among others, the intermediates PRibP and ribulose 1,5-bisphosphate (cf. ribose 5-phosphate and ribulose 5-phosphate of the pentose phosphate pathway). Enzymes of several pathways produce and utilize PRibP not only in ribonucleotide metabolism but also in the catabolism of phosphonates, i.e., compounds containing a carbon-phosphorus bond. Pathways for PRibP metabolism are found in all three domains of life, most prominently among organisms of the archaeal domain, where they have been identified either experimentally or by bioinformatic analysis within all of the four main taxonomic groups, Euryarchaeota, TACK, DPANN, and Asgard. Advances in molecular genetics of archaea have greatly improved the understanding of the physiology of PRibP metabolism, and reconciliation of molecular enzymology and three-dimensional structure analysis of enzymes producing or utilizing PRibP emphasize the versatility of the compound. Finally, PRibP is also an effector of several metabolic activities in many organisms, including higher organisms such as mammals. In the present review, we describe all aspects of PRibP metabolism, with emphasis on the biochemical, genetic, and physiological aspects of the enzymes that produce or utilize PRibP. The inclusion of high-resolution structures of relevant enzymes that bind PRibP provides evidence for the flexibility and importance of the compound in metabolism.
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12
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Hayer-Hartl M. From chaperonins to Rubisco assembly and metabolic repair. Protein Sci 2017; 26:2324-2333. [PMID: 28960553 DOI: 10.1002/pro.3309] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 09/21/2017] [Accepted: 09/25/2017] [Indexed: 01/13/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) mediates the fixation of atmospheric CO2 in photosynthesis by catalyzing the carboxylation of the 5-carbon sugar ribulose-1,5-bisphosphate (RuBP). Despite its pivotal role, Rubisco is an inefficient enzyme and thus has been a key target for bioengineering. However, efforts to increase crop yields by Rubisco engineering remain unsuccessful, due in part to the complex machinery of molecular chaperones required for Rubisco biogenesis and metabolic repair. While the large subunit of Rubisco generally requires the chaperonin system for folding, the evolution of the hexadecameric Rubisco from its dimeric precursor resulted in the dependence on an array of additional factors required for assembly. Moreover, Rubisco function can be inhibited by a range of sugar-phosphate ligands. Metabolic repair of Rubisco depends on remodeling by the ATP-dependent Rubisco activase and hydrolysis of inhibitors by specific phosphatases. This review highlights our work toward understanding the structure and mechanism of these auxiliary machineries.
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Affiliation(s)
- Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
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13
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Chen ZC, Peng WT, Li J, Liao H. Functional dissection and transport mechanism of magnesium in plants. Semin Cell Dev Biol 2017; 74:142-152. [PMID: 28822768 DOI: 10.1016/j.semcdb.2017.08.005] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/24/2017] [Accepted: 08/01/2017] [Indexed: 01/15/2023]
Abstract
Magnesium (Mg) is the second most abundant cation in plants, and, as such, is involved in numerous physiological and biochemical processes, including photosynthesis, enzyme activation, and synthesis of nucleic acids and proteins. Due to its relatively small ionic radius and large hydrated radius, Mg binds weakly to soil and root surfaces, and thereby is easily leached from soil. Mg deficiency not only affects crop productivity and quality, but also contributes to numerous chronic human diseases. Therefore, Mg nutrition in plants is an important issue in nutrition and food security. To acquire and maintain high concentrations of Mg, plants have evolved highly-efficient systems for Mg uptake, storage and translocation. Advances in the understanding of fundamental principles of Mg nutrition and physiology are required in order to improve Mg nutrient management, Mg stress diagnosis, and genetic marker assisted breeding efforts. The aims of this review are to highlight physiological and molecular mechanisms underlying Mg biological functions and to summarize recent developments in the elucidation of Mg transport systems in plants.
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Affiliation(s)
- Zhi Chang Chen
- Root Biology Center, Fujian Agriculture and Forestry University, Fujian, Fuzhou 350002, China.
| | - Wen Ting Peng
- Root Biology Center, Fujian Agriculture and Forestry University, Fujian, Fuzhou 350002, China; College of Resources and Environment, Fujian Agriculture and Forestry University, Fujian, Fuzhou 350002, China
| | - Jian Li
- Root Biology Center, Fujian Agriculture and Forestry University, Fujian, Fuzhou 350002, China; College of Life Sciences, Fujian Agriculture and Forestry University, Fujian, Fuzhou 350002, China
| | - Hong Liao
- Root Biology Center, Fujian Agriculture and Forestry University, Fujian, Fuzhou 350002, China
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14
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You C, Chen L, He H, Wu L, Wang S, Ding Y, Ma C. iTRAQ-based proteome profile analysis of superior and inferior Spikelets at early grain filling stage in japonica Rice. BMC PLANT BIOLOGY 2017; 17:100. [PMID: 28592253 PMCID: PMC5463490 DOI: 10.1186/s12870-017-1050-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/29/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Large-panicle rice varieties often fail to achieve their yield potential due to poor grain filling of late-flowering inferior spikelets (IS). The physiological and molecular mechanisms of poor IS grain filling, and whether an increase in assimilate supply could regulate protein abundance and consequently improve IS grain filling for japonica rice with large panicles is still partially understood. RESULTS A field experiment was performed with two spikelet removal treatments at anthesis in the large-panicle japonica rice line W1844, including removal of the top 1/3 of spikelets (T1) and removal of the top 2/3 of spikelets (T2), with no spikelet removal as a control (T0). The size, weight, setting rate, and grain filling rate of IS were significantly increased after spikelet removing. The biological functions of the differentially expressed proteins (DEPs) between superior and inferior spikelets as well as the response of IS to the removal of superior spikelets (SS) were investigated by using iTRAQ at 10 days post anthesis. A total of 159, 87, and 28 DEPs were identified from group A (T0-SS/T0-IS), group B (T0-SS/T2-IS), and group C (T2-IS/T0-IS), respectively. Among these, 104, 63, and 22 proteins were up-regulated, and 55, 24, and 6 proteins were down-regulated, respectively. Approximately half of these DEPs were involved in carbohydrate metabolism (sucrose-to-starch metabolism and energy metabolism) and protein metabolism (protein synthesis, folding, degradation, and storage). CONCLUSIONS Reduced endosperm cell division and decreased activities of key enzymes associated with sucrose-starch metabolism and nitrogen metabolism are mainly attributed to the poor sink strength of IS. In addition, due to weakened photosynthesis and respiration, IS are unable to obtain a timely supply of materials and energy after fertilization, which might be resulted in the stagnation of IS development. Finally, an increased abundance of 14-3-3 protein in IS could be involved in the inhibition of starch synthesis. The removal of SS contributed to transfer of assimilates to IS and enhanced enzymatic activities of carbon metabolism (sucrose synthase, starch branching enzyme, soluble starch synthase, and pullulanase) and nitrogen metabolism (aspartate amino transferase and alanine amino transferase), promoting starch and protein synthesis in IS. In addition, improvements in energy metabolism (greater abundance of pyrophosphate-fructose 6-phosphate 1-phosphotransferase) might be played a vital role in inducing the initiation of grain filling. These results collectively demonstrate that carbohydrate supply is the main cause of poor IS grain filling.
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Affiliation(s)
- Cuicui You
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Lin Chen
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Haibing He
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Liquan Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Shaohua Wang
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 People’s Republic of China
| | - Yanfeng Ding
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 People’s Republic of China
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
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15
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Ionic effects on microalgae harvest via microalgae-fungi co-pelletization. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2016.12.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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16
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Luo CS, Liang JR, Lin Q, Li C, Bowler C, Anderson DM, Wang P, Wang XW, Gao YH. Cellular responses associated with ROS production and cell fate decision in early stress response to iron limitation in the diatom Thalassiosira pseudonana. J Proteome Res 2014; 13:5510-23. [PMID: 25372880 PMCID: PMC4261981 DOI: 10.1021/pr5004664] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Investigation of how diatoms cope with the rapid fluctuations in iron bioavailability in marine environments may facilitate a better understanding of the mechanisms underlying their ecological success, in particular their ability to proliferate rapidly during favorable conditions. In this study, using in vivo biochemical markers and whole-cell iTRAQ-based proteomics analysis, we explored the cellular responses associated with reactive oxygen species (ROS) production and cell fate decision during the early response to Fe limitation in the centric diatom Thalassiosira pseudonana. Fe limitation caused a significant decrease in Photosystem (PS) II photosynthetic efficiency, damage to the photosynthetic electron transport chain in PS I, and blockage of the respiratory chain in complexes III and IV, which could all result in excess ROS accumulation. The increase in ROS likely triggered programmed cell death (PCD) in some of the Fe-limited cells through synthesis of a series of proteins involved in the delicate balance between pro-survival and pro-PCD factors. The results provide molecular-level insights into the major strategies that may be employed by T. pseudonana in response to Fe-limitation: the reduction of cell population density through PCD to reduce competition for available Fe, the reallocation of intracellular nitrogen and Fe to ensure survival, and an increase in expression of antioxidant and anti-PCD proteins to cope with stress.
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Affiliation(s)
- Chun-Shan Luo
- School of Life Sciences, Xiamen University , Xiamen 361102, People's Republic of China
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17
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Schada von Borzyskowski L, Rosenthal RG, Erb TJ. Evolutionary history and biotechnological future of carboxylases. J Biotechnol 2013; 168:243-51. [PMID: 23702164 DOI: 10.1016/j.jbiotec.2013.05.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 05/08/2013] [Accepted: 05/13/2013] [Indexed: 10/26/2022]
Abstract
Carbon dioxide (CO2) is a potent greenhouse gas whose presence in the atmosphere is a critical factor for global warming. At the same time atmospheric CO2 is also a cheap and readily available carbon source that can in principle be used to synthesize value-added products. However, as uncatalyzed chemical CO2-fixation reactions usually require quite harsh conditions to functionalize the CO2 molecule, not many processes have been developed that make use of CO2. In contrast to synthetical chemistry, Nature provides a multitude of different carboxylating enzymes whose carboxylating principle(s) might be exploited in biotechnology. This review focuses on the biochemical features of carboxylases, highlights possible evolutionary scenarios for the emergence of their reactivity, and discusses current, as well as potential future applications of carboxylases in organic synthesis, biotechnology and synthetic biology.
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18
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Li C, Zhu Y, Guo X, Sun C, Luo H, Song J, Li Y, Wang L, Qian J, Chen S. Transcriptome analysis reveals ginsenosides biosynthetic genes, microRNAs and simple sequence repeats in Panax ginseng C. A. Meyer. BMC Genomics 2013; 14:245. [PMID: 23577925 PMCID: PMC3637502 DOI: 10.1186/1471-2164-14-245] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Accepted: 04/02/2013] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Panax ginseng C. A. Meyer is one of the most widely used medicinal plants. Complete genome information for this species remains unavailable due to its large genome size. At present, analysis of expressed sequence tags is still the most powerful tool for large-scale gene discovery. The global expressed sequence tags from P. ginseng tissues, especially those isolated from stems, leaves and flowers, are still limited, hindering in-depth study of P. ginseng. RESULTS Two 454 pyrosequencing runs generated a total of 2,423,076 reads from P. ginseng roots, stems, leaves and flowers. The high-quality reads from each of the tissues were independently assembled into separate and shared contigs. In the separately assembled database, 45,849, 6,172, 4,041 and 3,273 unigenes were only found in the roots, stems, leaves and flowers database, respectively. In the jointly assembled database, 178,145 unigenes were observed, including 86,609 contigs and 91,536 singletons. Among the 178,145 unigenes, 105,522 were identified for the first time, of which 65.6% were identified in the stem, leaf or flower cDNA libraries of P. ginseng. After annotation, we discovered 223 unigenes involved in ginsenoside backbone biosynthesis. Additionally, a total of 326 potential cytochrome P450 and 129 potential UDP-glycosyltransferase sequences were predicted based on the annotation results, some of which may encode enzymes responsible for ginsenoside backbone modification. A BLAST search of the obtained high-quality reads identified 14 potential microRNAs in P. ginseng, which were estimated to target 100 protein-coding genes, including transcription factors, transporters and DNA binding proteins, among others. In addition, a total of 13,044 simple sequence repeats were identified from the 178,145 unigenes. CONCLUSIONS This study provides global expressed sequence tags for P. ginseng, which will contribute significantly to further genome-wide research and analyses in this species. The novel unigenes identified here enlarge the available P. ginseng gene pool and will facilitate gene discovery. In addition, the identification of microRNAs and the prediction of targets from this study will provide information on gene transcriptional regulation in P. ginseng. Finally, the analysis of simple sequence repeats will provide genetic makers for molecular breeding and genetic applications in this species.
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Affiliation(s)
- Chunfang Li
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Yingjie Zhu
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Xu Guo
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Chao Sun
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Hongmei Luo
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Jingyuan Song
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Ying Li
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Lizhi Wang
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Jun Qian
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Shilin Chen
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
- China Academy of Chinese Medical Sciences, Institute of Chinese Materia Medica, Beijing, 100700, China
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19
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Steinborn M, Suhanji M, Klüfers P. Mixed sugar-core–phosphate chelation of d-fructose 1,6-bisphosphate with the ReVO(tmen) metal fragment. Dalton Trans 2013; 42:5749-54. [DOI: 10.1039/c3dt32901a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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20
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Subunit interface dynamics in hexadecameric rubisco. J Mol Biol 2011; 411:1083-98. [PMID: 21745478 DOI: 10.1016/j.jmb.2011.06.052] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 06/27/2011] [Accepted: 06/30/2011] [Indexed: 11/23/2022]
Abstract
Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) plays an important role in the global carbon cycle as a hub for biomass. Rubisco catalyzes not only the carboxylation of RuBP with carbon dioxide but also a competing oxygenation reaction of RuBP with a negative impact on photosynthetic yield. The functional active site is built from two large (L) subunits that form a dimer. The octameric core of four L(2) dimers is held at each end by a cluster of four small (S) subunits, forming a hexadecamer. Each large subunit contacts more than one S subunit. These interactions exploit the dynamic flexibility of Rubisco, which we address in this study. Here, we describe seven different types of interfaces of hexadecameric Rubisco. We have analyzed these interfaces with respect to the size of the interface area and the number of polar interactions, including salt bridges and hydrogen bonds in a variety of Rubisco enzymes from different organisms and different kingdoms of life, including the Rubisco-like proteins. We have also performed molecular dynamics simulations of Rubisco from Chlamydomonas reinhardtii and mutants thereof. From our computational analyses, we propose structural checkpoints of the S subunit to ensure the functionality and/or assembly of the Rubisco holoenzyme. These checkpoints appear to fine-tune the dynamics of the enzyme in a way that could influence enzyme performance.
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21
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Satagopan S, Scott SS, Smith TG, Tabita FR. A Rubisco mutant that confers growth under a normally "inhibitory" oxygen concentration. Biochemistry 2009; 48:9076-83. [PMID: 19705820 DOI: 10.1021/bi9006385] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) is a globally significant biocatalyst that facilitates the removal and sequestration of CO2 from the biosphere. Rubisco-catalyzed CO2 reduction thus provides virtually all of the organic carbon utilized by living organisms. Despite catalyzing the rate-limiting step of photosynthetic and chemoautotrophic CO2 assimilation, Rubisco is markedly inefficient as the competition between O2 and CO2 for the same substrate limits the ability of aerobic organisms to obtain maximum amounts of organic carbon for CO2-dependent growth. Random and site-directed mutagenesis procedures were coupled with genetic selection to identify an "oxygen-insensitive" mutant cyanobacterial (Synechococcus sp. strain PCC 6301) Rubisco that allowed for CO2-dependent growth of a host bacterium at an oxygen concentration that inhibited growth of the host containing wild-type Synechococcus Rubisco. The mutant substitution, A375V, was identified as an intragenic suppressor of D103V, a negative mutant enzyme incapable of supporting autotrophic growth. Ala-375 (Ala-378 of spinach Rubisco) is a conserved residue in all form I (plant-like) Rubiscos. Structure-function analyses indicate that the A375V substitution decreased the enzyme's oxygen sensitivity (and not CO2/O2 specificity), possibly by rearranging a network of interactions in a fairly conserved hydrophobic pocket near the active site. These studies point to the potential of engineering plants and other significant aerobic organisms to fix CO2 unfettered by the presence of O2.
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Affiliation(s)
- Sriram Satagopan
- Department of Microbiology and the Plant Molecular Biology/Biotechnology Program, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210-1292, USA
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22
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The functional role of a conserved loop in EAL domain-based cyclic di-GMP-specific phosphodiesterase. J Bacteriol 2009; 191:4722-31. [PMID: 19376848 DOI: 10.1128/jb.00327-09] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
EAL domain-based cyclic di-GMP (c-di-GMP)-specific phosphodiesterases play important roles in bacteria by regulating the cellular concentration of the dinucleotide messenger c-di-GMP. EAL domains belong to a family of (beta/alpha)(8) barrel fold enzymes that contain a functional active site loop (loop 6) for substrate binding and catalysis. By examining the two EAL domain-containing proteins RocR and PA2567 from Pseudomonas aeruginosa, we found that the catalytic activity of the EAL domains was significantly altered by mutations in the loop 6 region. The impact of the mutations ranges from apparent substrate inhibition to alteration of oligomeric structure. Moreover, we found that the catalytic activity of RocR was affected by mutating the putative phosphorylation site (D56N) in the phosphoreceiver domain, with the mutant exhibiting a significantly smaller Michealis constant (K(m)) than that of the wild-type RocR. Hydrogen-deuterium exchange by mass spectrometry revealed that the decrease in K(m) correlates with a change of solvent accessibility in the loop 6 region. We further examined Acetobacter xylinus diguanylate cyclase 2, which is one of the proteins that contains a catalytically incompetent EAL domain with a highly degenerate loop 6. We demonstrated that the catalytic activity of the stand-alone EAL domain toward c-di-GMP could be recovered by restoring loop 6. On the basis of these observations and in conjunction with the structural data of two EAL domains, we proposed that loop 6 not only mediates the dimerization of EAL domain but also controls c-di-GMP and Mg(2+) ion binding. Importantly, sequence analysis of the 5,862 EAL domains in the bacterial genomes revealed that about half of the EAL domains harbor a degenerate loop 6, indicating that the mutations in loop 6 may represent a divergence of function for EAL domains during evolution.
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23
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Liggins JR, Gready JE. Putative functional role for the invariant aspartate 263 residue of Rhodospirillum rubrum Rubisco. Biochemistry 2009; 48:2226-36. [PMID: 19231887 DOI: 10.1021/bi802159e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although aspartate residue D263 of Rhodospirillum rubrum Rubisco is close to the active site and invariant in all reported Rubiscos, its possible functional and structural roles in Rubisco activity have not been investigated. We have mutagenised D263 to several selected amino acids (asparagine, alanine, serine, glutamate, and glutamine) to probe possible roles in facilitating proton movements within the active site and maintaining structural positioning of key active-site groups. The mutants have been characterized by kinetic methods and by differential scanning calorimetry (DSC) to examine the effects of the substitutions on the stability of the folded state. We show that D263 is essential for maintaining effective levels of catalysis with the mutations reducing carboxylation variously by up to 100-fold but having less than 10% effect on the carboxylase/oxygenase specificity of the catalytic reaction. Removing the charge of the residue 263 side chain significantly strengthens binding of the activating (carbamylating) CO(2) molecule. In contrast, a charge on the 263 site has only a small influence on binding of the positively charged Mg(2+) ion, suggesting that the local protein structure provides different shielding of the formal charges on the Mg(2+) ion and the epsilon-lysine group of K191. Interestingly, introduction of an internal cavity (D263S and D263A) and insertion of an extra -CH(2)- group (D263E and D263Q) have opposite effects on catalysis, the former relatively small and the latter much larger, suggesting that the extra side-chain group induces a specific structural distortion that inhibits formation of the transition state. As the DSC results show that the mutations only slightly increase the kinetic stability of the folded state, we conclude that the rate-limiting (activated) step of unfolding involves substantial unfolding of the structure but not in the region of site 263. In summary, interaction of D263 with H287 of a largely electrostatic nature appears critical for maintaining correct positioning of catalytic groups in the active site. The conservation of D263 can thus be accounted for by its contribution to the maintenance of a finely tuned structure in this region abutting the active site.
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Affiliation(s)
- John R Liggins
- Molecular Plant Physiology Group, Research School of Biological Sciences, John Curtin School of Medical Research, Australian National University, Canberra ACT 0200, Australia
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24
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Phylogenetic and evolutionary relationships of RubisCO and the RubisCO-like proteins and the functional lessons provided by diverse molecular forms. Philos Trans R Soc Lond B Biol Sci 2008; 363:2629-40. [PMID: 18487131 PMCID: PMC2606765 DOI: 10.1098/rstb.2008.0023] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RubisCO) catalyses the key reaction by which inorganic carbon may be assimilated into organic carbon. Phylogenetic analyses indicate that there are three classes of bona fide RubisCO proteins, forms I, II and III, which all catalyse the same reactions. In addition, there exists another form of RubisCO, form IV, which does not catalyse RuBP carboxylation or oxygenation. Form IV is actually a homologue of RubisCO and is called the RubisCO-like protein (RLP). Both RubisCO and RLP appear to have evolved from an ancestor protein in a methanogenic archaeon, and comprehensive analyses indicate that the different forms (I, II, III and IV) contain various subgroups, with individual sequences derived from representatives of all three kingdoms of life. The diversity of RubisCO molecules, many of which function in distinct milieus, has provided convenient model systems to study the ways in which the active site of this protein has evolved to accommodate necessary molecular adaptations. Such studies have proven useful to help provide a framework for understanding the molecular basis for many important aspects of RubisCO catalysis, including the elucidation of factors or functional groups that impinge on RubisCO carbon dioxide/oxygen substrate discrimination.
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25
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Andersson I, Backlund A. Structure and function of Rubisco. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2008; 46:275-91. [PMID: 18294858 DOI: 10.1016/j.plaphy.2008.01.001] [Citation(s) in RCA: 316] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Indexed: 05/18/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the major enzyme assimilating CO(2) into the biosphere. At the same time Rubisco is an extremely inefficient catalyst and its carboxylase activity is compromised by an opposing oxygenase activity involving atmospheric O(2). The shortcomings of Rubisco have implications for crop yield, nitrogen and water usage, and for the global carbon cycle. Numerous high-resolution crystal structures of different forms of Rubisco are now available, including structures of mutant enzymes. This review uses the information provided in these structures in a structure-based sequence alignment and discusses Rubisco function in the context of structural variations at all levels--amino acid sequence, fold, tertiary and quaternary structure--with an evolutionary perspective and an emphasis on the structural features of the enzyme that may determine its function as a carboxylase.
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Affiliation(s)
- Inger Andersson
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Husargatan 3, BMC Box 590, S-751 24 Uppsala, Sweden.
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26
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Mueller-Cajar O, Morell M, Whitney SM. Directed evolution of rubisco in Escherichia coli reveals a specificity-determining hydrogen bond in the form II enzyme. Biochemistry 2007; 46:14067-74. [PMID: 18004873 DOI: 10.1021/bi700820a] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) occupies a critical position in photosynthetic CO2-fixation and consequently has been the focus of intense study. Crystal-structure-guided site-directed mutagenesis studies have met with limited success in engineering kinetic improvements to Rubisco, highlighting our inadequate understanding of structural constraints at the atomic level that dictate the enzyme's catalytic chemistry. Bioselection provides an alternative random mutagenic approach that is useful for identifying and elucidating imperceptible structure-function relationships. Using the dimeric Form II Rubisco from Rhodospirillum rubrum, its gene (rbcM) was randomly mutated and introduced under positive selection into Escherichia coli cells metabolically engineered to be dependent on Rubisco to detoxify its substrate ribulose 1,5-bisphosphate. Thirteen colonies displaying improved fitness were isolated, and all were found to harbor mutations in rbcM at one of two codons, histidine-44 or aspartate-117, that are structurally adjacent amino acids located about 10 A from the active site. Biochemical characterization of the mutant enzymes showed the mutations reduced their CO2/O2 specificity by 40% and decreased their carboxylation turnover rate by 20-40%. Structural analyses showed histidine-44 and aspartate-117 form a hydrogen bond in R. rubrum Rubisco and that the residues are conserved among other Form II Rubiscos. This study demonstrated the utility of directed evolution in E. coli for identifying catalytically relevant residues (in particular nonobvious residues disconnected from active site residues) and their potential molecular interactions that influence Rubisco's catalytic chemistry.
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Affiliation(s)
- Oliver Mueller-Cajar
- Molecular Plant Physiology, Research School of Biological Sciences, Australian National University, P.O. Box 475, Canberra, Australian Capital Territory 2601, Australia
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27
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Hartman FC, Harpel MR. Chemical and genetic probes of the active site of D-ribulose-1,5-bisphosphate carboxylase/oxygenase: a retrospective based on the three-dimensional structure. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 67:1-75. [PMID: 8322615 DOI: 10.1002/9780470123133.ch1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- F C Hartman
- Biology Division, Oak Ridge National Laboratory, TN
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28
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Kreel NE, Tabita FR. Substitutions at methionine 295 of Archaeoglobus fulgidus ribulose-1,5-bisphosphate carboxylase/oxygenase affect oxygen binding and CO2/O2 specificity. J Biol Chem 2006; 282:1341-51. [PMID: 17074752 DOI: 10.1074/jbc.m609399200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Archaeoglobus fulgidus RbcL2, a form III ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), exhibits unique properties not found in other well studied form I and II Rubiscos, such as optimal activity from 83 to 93 degrees C and an extremely high kcat value (23 s-1). More interestingly, this protein is unusual in that exposure or assay in the presence of oxygen and high levels of CO2 resulted in substantial loss (85-90%) of activity compared with assays performed under strictly anaerobic conditions. Kinetic studies indicated that A. fulgidus RbcL2 possesses an unusually high affinity for oxygen (Ki=5 microM); O2 is a competitive inhibitor with respect to CO2, yet the high affinity for O2 presumably accounts for the inability of high levels of CO2 to prevent inhibition. Comparative bioinformatic analyses of available archaeal Rubisco sequences were conducted to provide clues as to why the RbcL2 protein might possess such a high affinity for oxygen. These analyses suggested the potential importance of several unique residues, as did additional analyses within the context of available form I-III Rubisco structures. One residue unique to archaeal proteins (Met-295) was of particular interest because of its proximity to known active-site residues. Recombinant M295D A. fulgidus Rubisco was less sensitive to oxygen compared with the wild-type enzyme. This residue, along with other potential changes in conserved residues of form III Rubiscos, may provide an understanding as to how Rubisco may have evolved to function in the presence of air.
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Affiliation(s)
- Nathaniel E Kreel
- Department of Microbiology and the Plant Molecular Biology/Biotechnology Program, Ohio State University, Columbus, Ohio 43210-1292, USA
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29
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Carré-Mlouka A, Méjean A, Quillardet P, Ashida H, Saito Y, Yokota A, Callebaut I, Sekowska A, Dittmann E, Bouchier C, de Marsac NT. A New Rubisco-like Protein Coexists with a Photosynthetic Rubisco in the Planktonic Cyanobacteria Microcystis. J Biol Chem 2006; 281:24462-71. [PMID: 16737967 DOI: 10.1074/jbc.m602973200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two genes encoding proteins related to large subunits of Rubisco were identified in the genome of the planktonic cyanobacterium Microcystis aeruginosa PCC 7806 that forms water blooms worldwide. The rbcL(I) gene belongs to the form I subfamily typically encountered in cyanobacteria, green algae, and land plants. The second and newly discovered gene is of the form IV subfamily and widespread in the Microcystis genus. In M. aeruginosa PCC 7806 cells, the expression of both rbcL(I) and rbcL(IV) is sulfur-dependent. The purified recombinant RbcL(IV) overexpressed in Escherichia coli cells did not display CO(2) fixation activity but catalyzed enolization of 2,3-diketo-5-methylthiopentyl-1-phosphate, and the rbcL(IV) gene rescued a Bacillus subtilis MtnW-deficient mutant. Therefore, the Microcystis RbcL(IV) protein functions both in vitro and in vivo and might be involved in a methionine salvage pathway. Despite variations in the amino acid sequences, RbcL(IV) shares structural similarities with all members of the Rubisco superfamily. Invariant amino acids within the catalytic site may thus represent the minimal set for enolization, whereas variations, especially located in loop 6, may account for the limitation of the catalytic reaction to enolization. Even at low protein concentrations in vitro, the recombinant RbcL(IV) assembles spontaneously into dimers, the minimal unit required for Rubisco forms I-III activity. The discovery of the coexistence of RbcL(I) and RbcL(IV) in cyanobacteria, the ancestors of chloroplasts, enlightens episodes of the chaotic evolutionary history of the Rubiscos, a protein family of major importance for life on Earth.
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Affiliation(s)
- Alyssa Carré-Mlouka
- Département de Microbiologie, Unité des Cyanobactéries (CNRS-URA 2172) and Plate-forme Génomique-Pasteur Génopole Ile de France, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
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30
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Li H, Sawaya MR, Tabita FR, Eisenberg D. Crystal structure of a RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum. Structure 2005; 13:779-89. [PMID: 15893668 DOI: 10.1016/j.str.2005.02.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2004] [Revised: 02/17/2005] [Accepted: 02/19/2005] [Indexed: 11/24/2022]
Abstract
Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzes the incorporation of atmospheric CO(2) into ribulose 1,5-bisphosphate (RuBP). RuBisCOs are classified into four forms based on sequence similarity: forms I, II and III are bona fide RuBisCOs; form IV, also called the RuBisCO-like protein (RLP), lacks several of the substrate binding and catalytic residues and does not catalyze RuBP-dependent CO(2) fixation in vitro. To contribute to understanding the function of RLPs, we determined the crystal structure of the RLP from Chlorobium tepidum. The overall structure of the RLP is similar to the structures of the three other forms of RuBisCO; however, the active site is distinct from those of bona fide RuBisCOs and suggests that the RLP is possibly capable of catalyzing enolization but not carboxylation. Bioinformatic analysis of the protein functional linkages suggests that this RLP coevolved with enzymes of the bacteriochlorophyll biosynthesis pathway and may be involved in processes related to photosynthesis.
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Affiliation(s)
- Huiying Li
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Box 951570, Los Angeles, California 90095, USA
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31
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Aparicio R, Ferreira ST, Polikarpov I. Closed Conformation of the Active Site Loop of Rabbit Muscle Triosephosphate Isomerase in the Absence of Substrate: Evidence of Conformational Heterogeneity. J Mol Biol 2003; 334:1023-41. [PMID: 14643664 DOI: 10.1016/j.jmb.2003.10.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The active site loop of triosephosphate isomerase (TIM) exhibits a hinged-lid motion, alternating between the two well defined "open" and "closed" conformations. Until now the closed conformation had only been observed in protein complexes with substrate analogues. Here, we present the first rabbit muscle apo TIM structure, refined to 1.5A resolution, in which the active site loop is either in the open or in the closed conformation in different subunits of the enzyme. In the closed conformation described here, the lid loop residues participate in stabilizing hydrogen bonds characteristic of holo TIM structures, whereas chemical interactions observed in the open loop conformation are similar to those found in the apo structures of TIM. In the closed conformation, a number of water molecules are observed at the projected ligand atom positions that are hydrogen bonded to the active site residues. Additives used during crystallization (DMSO and Tris molecules and magnesium atoms) were modeled in the electron density maps. However, no specific binding of these molecules is observed at, or close to, the active site and the lid loop. To further investigate this unusual closed conformation of the apo enzyme, two more rabbit muscle TIM structures, one in the same and another in a different crystal form, were determined. These structures present the open lid conformation only, indicating that the closed conformation cannot be explained by crystal contact effects. To rationalize why the active site loop is closed in the absence of ligand in one of the subunits, extensive comparison with previously solved TIM structures was carried out, supported by the bulk of available experimental information about enzyme kinetics and reaction mechanism of TIM. The observation of both open and closed lid conformations in TIM crystals might be related to a persistent conformational heterogeneity of this protein in solution.
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Affiliation(s)
- Ricardo Aparicio
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador SãoCarlense, 400, São Carlos, SP 13560-970, Brazil
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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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33
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Low JC, Tu SC. Functional roles of conserved residues in the unstructured loop of Vibrio harveyi bacterial luciferase. Biochemistry 2002; 41:1724-31. [PMID: 11827516 DOI: 10.1021/bi011958p] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Residues 257-291 of the Vibrio harveyi bacterial luciferase alpha subunit comprise a highly conserved, protease-labile, disordered loop region, most of which is unresolved in the previously determined X-ray structures of the native enzyme. This loop region has been shown to display a time- dependent proteolysis resistance upon single catalytic turnover and was postulated to undergo conformational changes during catalysis ([AbouKhair, N. K., Ziegler, M. M., and Baldwin, T. O. (1985) Biochemistry 24, 3942-3947]. To investigate the role of this region in catalysis, we have performed site-specific mutations of different conserved loop residues. In comparison with V(max) and V(max)/K(m,flavin) of the native luciferase, the bioluminescence activities of alphaG284P were decreased to 1-2% whereas those of alphaG275P and alphaF261D were reduced by 4-6 orders of magnitude. Stopped-flow results indicate that both alphaG275P and alphaF261D were able to form the 4a-hydroperoxy-FMN intermediate II but at lower yields. Both mutants also had enhanced rates for the intermediate II nonproductive dark decay and significantly compromised abilities to oxidize the decanal substrate. Additional mutations were introduced into the alphaG275 and alphaF261 positions, and the activities of the resulting mutants were characterized. Results indicate that the torsional flexibility of the alphaG275 residue and the bulky and hydrophobic nature of the alphaF261 residue were critical to the luciferase activity. Our results also support a functional role for the alpha subunit unstructured loop itself, possibly by serving as a mobile gating mechanism in shielding critical intermediates (including the excited flavin emitter) from exposure to medium.
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Affiliation(s)
- John C Low
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA
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Harpel MR, Larimer FW, Hartman FC. Multifaceted roles of Lys166 of ribulose-bisphosphate carboxylase/oxygenase as discerned by product analysis and chemical rescue of site-directed mutants. Biochemistry 2002; 41:1390-7. [PMID: 11802742 DOI: 10.1021/bi011828g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ab initio calculations [King, W. A., et al. (1998) Biochemistry 37, 15414-15422] of an active-site mimic of D-ribulose-1,5-bisphosphate carboxylase/oxygenase suggest that active-site Lys166 plays a role in carboxylation in addition to its functions in the initial deprotonation and final protonation steps. To test this postulate, the turnover of 1-(3)H-labeled D-ribulose 1,5-bisphosphate (RuBP) by impaired position-166 mutants was characterized. Although these mutants catalyze slow enolization of RuBP, most of the RuBP-enediol undergoes beta-elimination of phosphate to form 2,3-pentodiulose 5-phosphate, signifying deficiencies in normal carboxylation and oxygenation. Much of the remaining RuBP-enediol is carboxylated but forms pyruvate, rather than 3-phospho-D-glycerate, due to incapacity in protonation of the terminal aci-acid intermediate. As a further test of the postulate, the effects of subtle perturbation of the Lys166 side chain on the carboxylation/oxygenation partitioning ratio (tau) were determined. To eliminate a chemically reactive site, Cys58 was replaced by a seryl residue without any loss of activity. The virtually inactive K166C-C58S double mutant was chemically rescued by aminoethylation or aminopropylation to reinsert a lysyl-like side chain at position 166. Relative to the wild-type value, tau for the aminoethylated enzyme was increased by approximately 30%, and tau for the aminopropylated enzyme was decreased by approximately 80%. Thus, two lines of experimentation support the theoretically based conclusion for the importance of Lys166 in the reaction of RuBP-enediol with gaseous substrates.
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Affiliation(s)
- Mark R Harpel
- Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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35
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Kitano K, Maeda N, Fukui T, Atomi H, Imanaka T, Miki K. Crystal structure of a novel-type archaeal rubisco with pentagonal symmetry. Structure 2001; 9:473-81. [PMID: 11435112 DOI: 10.1016/s0969-2126(01)00608-6] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the key enzyme of the Calvin-Benson cycle and catalyzes the primary reaction of CO2 fixation in plants, algae, and bacteria. Rubiscos have been so far classified into two types. Type I is composed of eight large subunits (L subunits) and eight small subunits (S subunits) with tetragonal symmetry (L8S8), but type II is usually composed only of two L subunits (L2). Recently, some genuinely active Rubiscos of unknown physiological function have been reported from archaea. RESULTS The crystal structure of Rubisco from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 (Tk-Rubisco) was determined at 2.8 A resolution. The enzyme is composed only of L subunits and showed a novel (L2)5 decameric structure. Compared to previously known type I enzymes, each L2 dimer is inclined approximately 16 degrees to form a toroid-shaped decamer with its unique L2-L2 interfaces. Differential scanning calorimetry (DSC), circular dichroism (CD), and gel permeation chromatography (GPC) showed that Tk-Rubisco maintains its secondary structure and decameric assembly even at high temperatures. CONCLUSIONS The present study provides the first structure of an archaeal Rubisco, an unprecedented (L2)5 decamer. Biochemical studies indicate that Tk-Rubisco maintains its decameric structure at high temperatures. The structure is distinct from type I and type II Rubiscos and strongly supports that Tk-Rubisco should be classified as a novel type III Rubisco.
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Affiliation(s)
- K Kitano
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, 606-8502, Kyoto, Japan
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36
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Darensbourg DJ, Frost BJ, Larkins DL. An experimental and theoretical investigation of the carbon dioxide insertion process into the tungsten-nitrogen bond of an anionic W(0) complex. Inorg Chem 2001; 40:1993-9. [PMID: 11304140 DOI: 10.1021/ic001006s] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The pyridine bound 2-aminopyridine (2APH) derivative of tungsten pentacarbonyl has been prepared from photogenerated W(CO)5THF and 2APH. Deprotonation of the distal amine group by sodium hydride has provided two complexes, [Na][W(CO)5(2AP)] and [Na]2[W(CO)4(2AP)]2. Both complexes have been characterized by X-ray crystallography with the monomeric derivative being crystallized as its [Na2(18-crown-6)][W(CO)5(2AP)]2 salt which exhibits strong Na+...-NH interactions. Photolysis of W(CO)6 in the presence of excess 2-aminopyridine in THF has led to an efficient synthesis of the chelated neutral derivative, W(CO)4(2APH).2APH, where the extra equivalent of 2APH is hydrogen bonded to its bound counterpart. The 2-aminopyridine molecule of solvation was almost quantitatively removed via aqueous washings. Deprotonation of W(CO)4(2APH) with NaH afforded the amidopyridine derivative which was shown to rapidly undergo reaction with CO2 to yield the chelated carbamate complex, W(CO)4(OC(O)2AP)-. Nevertheless, because of the presence of small quantities of free 2-aminopyridine during the reactions with CO2, we have not been able to conclusively rule out participation by a ligand substitution process involving NC5H4NHCOOH. Ab initio computations were found to substantiate many of these experimental observations. That is, in the monodentate bound W(CO)5(2APH) derivative, binding through the pyridine nitrogen atom is favored by about 29 kJ/mol over the amine nitrogen atom, whereas the opposite site for binding is preferred for the deprotonated amido analogue, W(CO)5(2AP)-. Furthermore, both forms of W(CO)5(2AP)- were found to be more stable than the chelated tungsten tetracarbonyl anion plus CO. On the other hand, CO2 insertion into the W(CO)4(2AP)- anion to provide the chelated carbamate, W(CO)4(OC(O)2AP)-, was thermodynamically favored by >110 kJ/mol. Finally, both experimental and theoretical studies were inconclusive with regard to identifying reaction intermediates during the CO2 insertion pathway which involve prior interactions of CO2 at the amido nitrogen center.
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Affiliation(s)
- D J Darensbourg
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, USA
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37
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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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38
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Duff AP, Andrews TJ, Curmi PM. The transition between the open and closed states of rubisco is triggered by the inter-phosphate distance of the bound bisphosphate. J Mol Biol 2000; 298:903-16. [PMID: 10801357 DOI: 10.1006/jmbi.2000.3724] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
d-Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) catalyses the central CO(2)-fixing reaction of photosynthesis in a complex, multiple-step process. Several structures of rubisco complexed with substrate analogues, inhibitors and products have been determined by X-ray crystallography. The structures fall into two well-defined and distinct states. The active site is either "open" or "closed". The timing and mechanism of the transition between these two states have been uncertain. We solved the crystal structure of unactivated (metal-free) rubisco from tobacco with only inorganic phosphate bound and conclude that phosphate binding per se does not trigger closure, as it does in the similarly structured enzyme, triosephosphate isomerase. Comparison of all available rubisco structures suggests that, instead, the distance between the terminal phosphates (P1 and P2) of the bisphosphate ligand is the trigger: if that distance is less than 9.1 A, then the active site closes; if it is greater than 9.4 A then the enzyme remains open. Shortening of the inter-phosphate distance results from the ligand binding in a more curved conformation when O atoms of the ligand's sugar backbone interact either with the metal, if it is present, or with charged groups in the metal-binding site, if the metal is absent. This shortening brings the P1 phosphate into hydrogen bonding contact with Thr65. Thr65 exists in two discrete states related by a rotation of the backbone psi torsion angle. This rotation is coupled to domain rotation and hence to active site closure. Rotation of the side-chain of Thr65 also affects the C-terminal strand of large subunit which packs against Loop 6 after closure. The position of the C-terminal strand in the closed state is stabilised by multiple polar interactions with a distinctive highly-charged latch site involving the side-chain of Asp473. In the open state, this latch site may be occupied instead by phosphorylated anions.
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Affiliation(s)
- A P Duff
- Initiative in Biomolecular Structure, School of Physics University of New South Wales, Sydney, NSW 2052, Australia
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39
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McMillan FM, Cahoon M, White A, Hedstrom L, Petsko GA, Ringe D. Crystal structure at 2.4 A resolution of Borrelia burgdorferi inosine 5'-monophosphate dehydrogenase: evidence of a substrate-induced hinged-lid motion by loop 6. Biochemistry 2000; 39:4533-42. [PMID: 10758003 DOI: 10.1021/bi992645l] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conversion of inosine 5'-monophosphate (IMP) to xanthosine 5'-monophosphate (XMP) is the committed and rate-limiting reaction in de novo guanine nucleotide biosynthesis. Inosine 5'- monophosphate dehydrogenase (IMPDH) is the enzyme that catalyzes the oxidation of IMP to XMP with the concomitant reduction of nicotinamide adenine dinucleotide (from NAD(+) to NADH). Because of its critical role in purine biosynthesis, IMPDH is a drug design target for anticancer, antiinfective, and immunosuppressive chemotherapy. We have determined the crystal structure of IMPDH from Borrelia burgdorferi, the bacterial spirochete that causes Lyme disease, with a sulfate ion bound in the IMP phosphate binding site. This is the first structure of IMPDH in the absence of substrate or cofactor where the active-site loop (loop 6), which contains the essential catalytic residue Cys 229, is clearly defined in the electron density. We report that a seven residue region of loop 6, including Cys229, is tilted more than 6 A away from its position in substrate- or substrate analogue-bound structures of IMPDH, suggestive of a conformational change. The location of this loop between beta6 and alpha6 links IMPDH to a family of beta/alpha barrel enzymes known to utilize this loop as a functional lid during catalysis. Least-squares minimization, root-mean-square deviation analysis, and inspection of the molecular surface of the loop 6 region in the substrate-free B. burgdorferi IMPDH and XMP-bound Chinese hamster IMPDH show that loop 6 follows a similar pattern of hinged rigid-body motion and indicates that IMPDH may be using loop 6 to bind and sequester substrate and to recruit an essential catalytic residue.
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Affiliation(s)
- F M McMillan
- The Rosenstiel Basic Medical Sciences Research Center and Department of Biochemistry, Brandeis University, Waltham, Massachussetts 02454, USA
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40
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41
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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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42
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Sugawara H, Yamamoto H, Shibata N, Inoue T, Okada S, Miyake C, Yokota A, Kai Y. Crystal structure of carboxylase reaction-oriented ribulose 1, 5-bisphosphate carboxylase/oxygenase from a thermophilic red alga, Galdieria partita. J Biol Chem 1999; 274:15655-61. [PMID: 10336462 DOI: 10.1074/jbc.274.22.15655] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco, EC 4.1.1. 39) obtained from a thermophilic red alga Galdieria partita has the highest specificity factor of 238 among the Rubiscos hitherto reported. Crystal structure of activated Rubisco from G. partita complexed with the reaction intermediate analogue, 2-carboxyarabinitol 1,5-bisphosphate (2-CABP) has been determined at 2.4-A resolution. Compared with other Rubiscos, different amino residues bring the structural differences in active site, which are marked around the binding sites of P-2 phosphate of 2-CABP. Especially, side chains of His-327 and Arg-295 show the significant differences from those of spinach Rubisco. Moreover, the side chains of Asn-123 and His-294 which are reported to bind the substrate, ribulose 1,5-bisphosphate, form hydrogen bonds characteristic of Galdieria Rubisco. Small subunits of Galdieria Rubisco have more than 30 extra amino acid residues on the C terminus, which make up a hairpin-loop structure to form many interactions with the neighboring small subunits. When the structures of Galdieria and spinach Rubiscos are superimposed, the hairpin region of the neighboring small subunit in Galdieria enzyme and apical portion of insertion residues 52-63 characteristic of small subunits in higher plant enzymes are almost overlapped to each other.
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Affiliation(s)
- H Sugawara
- Department of Materials Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan
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Watson GM, Yu JP, Tabita FR. Unusual ribulose 1,5-bisphosphate carboxylase/oxygenase of anoxic Archaea. J Bacteriol 1999; 181:1569-75. [PMID: 10049390 PMCID: PMC93548 DOI: 10.1128/jb.181.5.1569-1575.1999] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The predominant pool of organic matter on earth is derived from the biological reduction and assimilation of carbon dioxide gas, catalyzed primarily by the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO). By virtue of its capacity to use molecular oxygen as an alternative and competing gaseous substrate, the catalytic efficiency of RubisCO and the enzyme's ability to assimilate CO2 may be severely limited, with consequent environmental and agricultural effects. Recent genomic sequencing projects, however, have identified putative RubisCO genes from anoxic Archaea. In the present study, these potential RubisCO sequences, from Methanococcus jannaschii and Archaeoglobus fulgidus, were analyzed in order to ascertain whether such sequences might encode functional proteins. We also report the isolation and properties of recombinant RubisCO using sequences obtained from the obligately anaerobic hyperthermophilic methanogen M. jannaschii. This is the first description of an archaeal RubisCO sequence; this study also represents the initial characterization of a RubisCO molecule that has evolved in the absence of molecular oxygen. The enzyme was shown to be a homodimer whose deduced sequence, along with other recently obtained archaeal RubisCO sequences, differs substantially from those of known RubisCO molecules. The recombinant M. jannaschii enzyme has a somewhat low, but reasonable kcat, however, unlike previously isolated RubisCO molecules, this enzyme is very oxygen sensitive yet it is stable to hyperthermal temperatures and catalyzes the formation of the expected carboxylation product. Despite inhibition by oxygen, this unusual RubisCO still catalyzes a weak yet demonstrable oxygenase activity, with perhaps the lowest capacity for CO2/O2 discrimination ever encountered for any RubisCO.
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Affiliation(s)
- G M Watson
- Department of Microbiology and The Ohio State Plant Molecular Biology/Biotechnology, Ohio State Biochemistry, and Ohio State Molecular Cellular and Developmental Biology Programs, The Ohio State University, Columbus, Ohio 43210-1292, USA
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44
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Carbon dioxide and metal centres: from reactions inspired by nature to reactions in compressed carbon dioxide as solvent. Coord Chem Rev 1999. [DOI: 10.1016/s0010-8545(98)00200-8] [Citation(s) in RCA: 140] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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45
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King WA, Gready JE, Andrews TJ. Quantum chemical analysis of the enolization of ribulose bisphosphate: the first hurdle in the fixation of CO2 by Rubisco. Biochemistry 1998; 37:15414-22. [PMID: 9799503 DOI: 10.1021/bi981598e] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A study, using ab initio quantum chemical methods, of the first step in the reaction mechanism of Rubisco, the enolization of the substrate, ribulose bisphosphate, is reported. This is the first such study that takes into account the likely roles of critical features within the active site. On the basis of molecular dynamics relaxation of the complex between activated enzyme and substrate using X-ray crystallographic structures as starting coordinates, a 29-atom fragment that mimicked the active site was constructed. States along a proposed reaction pathway were calculated using density functional theory and Moller-Plesset second-order perturbation theory. The results are consistent with the postulate that the base that abstracts the C3 proton of ribulose bisphosphate is the metal-stabilized carbamate of Lys-201 formed during the activation process. The calculations suggest that the active-site residue, Lys-175, is charged before enolization commences and they indicate a possible means by which the enzyme directs the incoming CO2 to attack the C2 carbon atom of the enediol, rather than the chemically very similar C3 atom.
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Affiliation(s)
- W A King
- Computational Molecular Biology and Drug Design Group, John Curtin School of Medical Research, Australian National University, Canberra
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46
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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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Harpel MR, Larimer FW, Hartman FC. Multiple catalytic roles of His 287 of Rhodospirillum rubrum ribulose 1,5-bisphosphate carboxylase/oxygenase. Protein Sci 1998; 7:730-8. [PMID: 9541405 PMCID: PMC2143942 DOI: 10.1002/pro.5560070322] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Active-site His 287 of Rhodospirillum rubrum ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase interacts with the C3-hydroxyl of bound substrate or reaction-intermediate analogue (CABP), water molecules, and ligands for the activator metal-ion (Andersson I, 1996, J Mol Biol 259:160-174; Taylor TC, Andersson I, 1997, J Mol Biol 265:432-444). To test structure-based postulates of catalytic functionality, His 287 was replaced with Asn or Gln. The mutants are not affected adversely in subunit assembly, activation (binding of Mg2+ and carbamylation of Lys 191), or recognition of phosphorylated ligands; they bind CABP with even greater tenacity than does wild-type enzyme. H287N and H287Q are severely impaired in catalyzing overall carboxylation (approximately 10(3)-fold and > 10(5)-fold, respectively) and enolization (each mutant below threshold for detection) of RuBP. H287N preferentially catalyzes decarboxylation of carboxylated reaction intermediate instead of forward processing to phosphoglycerate. Analysis of RuBP turnover that occurs at high concentrations of mutants over extended time periods reveal > 10-fold reduced CO2/O2 specificities, elevated misprotonation of the enediol intermediate, and misprocessing of the oxygenated intermediate of the oxygenase pathway. These results are consistent with multifaceted roles for His 287 in promoting enediol formation, enediol tautomerization, and forward-processing of carboxylated intermediate.
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Affiliation(s)
- M R Harpel
- Protein Engineering Program, Life Sciences Division, Oak Ridge National Laboratory, Tennessee 37831-8080, USA
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48
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Chène P, Day AG, Fersht AR. Role of isoleucine-164 at the active site of rubisco from Rhodospirillum rubrum. Biochem Biophys Res Commun 1997; 232:482-6. [PMID: 9125206 DOI: 10.1006/bbrc.1997.6318] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Isoleucine-164 is in Van der Waals contact with two ligands (lysine-191 and aspartate-193) of the activator magnesium ion at the active site of ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum. To observe the effect of mutations in the second sphere of coordination of the metal ion, isoleucine-164 was replaced by threonine, asparagine, and aspartate. All the mutant enzymes obtained exhibit a low carboxylase activity. Ile164Asp has less than 0.1% of the wild-type carboxylase activity, Ile164Thr and Ile164Asn 6 and 1%, respectively. The mutations increase the Km(RuBP) and decrease the Kcat of the mutated enzymes. The Kcat/Km(RuBP) of Ile164Thr and Ile164Asn are 40- and 900-fold lower than wild-type, respectively. The alteration of the hydrophobic contacts between isoleucine-164 and the metal ion ligands modifies the binding of the magnesium ion and the stabilization of the 2-carboxy-arabinitol 1,5-bisphosphate and decreases the specificity factor, tau.
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Affiliation(s)
- P Chène
- Genencor International, South San Francisco, California 94127, USA
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Tapia O, Andrés J, Safont VS. Inactivation of Ribulose-1,5-bisphosphate Carboxylase/Oxygenase during Catalysis. A Theoretical Study of Related Transition Structures. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp951661z] [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)
- O. Tapia
- Department of Physical Chemistry, Uppsala University, Box 532, S-75121 Uppsala, Sweden
| | - J. Andrés
- Department of Experimental Sciences, University Jaume I, Box 242, 12080 Castelló, Spain
| | - V. S. Safont
- Department of Experimental Sciences, University Jaume I, Box 242, 12080 Castelló, Spain
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Shikanai T, Foyer CH, Dulieu H, Parry MA, Yokota A. A point mutation in the gene encoding the Rubisco large subunit interferes with holoenzyme assembly. PLANT MOLECULAR BIOLOGY 1996; 31:399-403. [PMID: 8756604 DOI: 10.1007/bf00021801] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), a key enzyme of photosynthetic CO2 fixation, is composed of 8 large and 8 small subunits. The Rubisco-deficient Nicotiana tabacum mutant Sp25 is able to synthesize the peptides for both subunits but does not contain any active holoenzyme. The phenotype is maternally inherited and thus caused by a mutation in the chloroplast genome, which also encodes the Rubisco large subunit. A comparison of the nucleotide sequences of the large subunit gene of the Sp25 mutant with that of the wild-type tobacco revealed a single nucleotide change in the Sp25 mutant. This resulted in an amino acid substitution at Gly-322, which was replaced by serine.
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Affiliation(s)
- T Shikanai
- Plant Molecular Physiology Lab., RITE, Kyoto, Japan
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