59 results found
McFarlane C, Murray J, 2020, A sensitive coupled enzyme assay for measuring kinase and ATPase kinetics using ADP-specific hexokinase, Bio-protocol, Vol: 10, Pages: 1-10, ISSN: 2331-8325
Kinases and ATPases perform essential biological functions in metabolism and regulation.Activity of these enzymes is commonly measured by coupling ATP consumption to the synthesis of adetectable product. For most assay systems the ATP concentration during the reaction is unknown,compromising the precision of the assay. Using the ADP-specific hexokinase (ADP-HK) from the thermophilic archaeon Thermococcus litoralisthe protocol outlined here allows real time coupling of ATP consumption to downstream signal changeenabling accurate kinetic measurements. ADP-HK phosphorylates glucose that is then used by glucose6-phosphate dehydrogenase to reduce NAD+ to NADH which can be measured at 340 nm. We haveshown this assay to be sensitive to the detection of micromole quantities of ADP with no detectablebackground from ATP.
Trinugroho JP, Beckova M, Shao S, et al., 2020, Chlorophyll f synthesis by a super-rogue photosystem II complex (vol 6, pg 238, 2020), NATURE PLANTS, Vol: 6, Pages: 427-427, ISSN: 2055-026X
Trinugroho J, Bečková M, Shao S, et al., 2020, Chlorophyll f synthesis by a super-rogue photosystem II complex, Nature Plants, Vol: 6, Pages: 238-244, ISSN: 2055-026X
Certain cyanobacteria synthesize chlorophyll molecules (Chl d and Chl f) that absorb in the far-red region of the solar spectrum, thereby extending the spectral range of photosynthetically active radiation1,2. The synthesis and introduction of these far-red chlorophylls into the photosynthetic apparatus of plants might improve the efficiency of oxygenic photosynthesis, especially in far-red enriched environments, such as in the lower regions of the canopy3. Production of Chl f requires the ChlF subunit, also known as PsbA4 (ref. 4) or super-rogue D1 (ref. 5), a paralogue of the D1 subunit of photosystem II (PSII) which, together with D2, bind cofactors involved in the light-driven oxidation of water. Current ideas suggest that ChlF oxidizes Chl a to Chl f in a homodimeric ChlF reaction centre (RC) complex and represents a missing link in the evolution of the heterodimeric D1/D2 RC of PSII (refs. 4,6). However, unambiguous biochemical support for this proposal is lacking. Here, we show that ChlF can substitute for D1 to form modified PSII complexes capable of producing Chl f. Remarkably, mutation of just two residues in D1 converts oxygen-evolving PSII into a Chl f synthase. Overall, we have identified a new class of PSII complex, which we term ‘super-rogue’ PSII, with an unexpected role in pigment biosynthesis rather than water oxidation.
McFarlane C, Shah N, Kabasakal B, et al., 2019, Structural basis of light-induced redox regulation in the Calvin-Benson cycle in cyanobacteria, Proceedings of the National Academy of Sciences of USA, Vol: 116, Pages: 20984-20990, ISSN: 0027-8424
Plants, algae, and cyanobacteria fix carbon dioxide to organic carbon with the Calvin-Benson (CB) cycle. Phosphoribulokinase (PRK) and glyceraldehyde 3 phosphate dehydrogenase (GAPDH) are essential Calvin-Benson cycle enzymes that control substrate availability for the carboxylation enzyme Rubisco. PRK consumes ATP to produce the Rubisco substrate ribulose bisphosphate (RuBP). GAPDH catalyses the reduction step of the CB cycle with NADPH to produce the sugar, glyceraldehyde 3-phosphate (GAP), which is used for regeneration of RuBP and is the main exit point of the cycle. GAPDH and PRK are co-regulated by the redox state of a conditionally disordered protein CP12, which forms a ternary complex with both enzymes. However, the structural basis of Calvin-Benson cycle regulation by CP12 is unknown. Here we show how CP12 modulates the activity of both GAPDH and PRK. Using thermophilic cyanobacterial homologues, we solve crystal structures of GAPDH with different cofactors and CP12 bound, and the ternary GAPDH-CP12-PRK complex by electron cryo-microscopy, we reveal that formation of the N-terminal disulfide pre-orders CP12 prior to binding the PRK active site, which is resolved in complex with CP12. We find that CP12 binding to GAPDH influences substrate accessibility of all GAPDH active sites in the binary and ternary inhibited complexes. Our structural and biochemical data explain how CP12 integrates responses from both redox state and nicotinamide dinucleotide availability to regulate carbon fixation.
Varghese F, Kabasakal BV, Cotton CA, et al., 2019, A low-potential terminal oxidase associated with the iron-only nitrogenase from the nitrogen-fixing bacterium Azotobacter vinelandii, Journal of Biological Chemistry, Vol: 294, Pages: 9367-9376, ISSN: 0021-9258
The biological route for nitrogen gas entering the biosphere is reduction to ammonia by the nitrogenase enzyme, which is inactivated by oxygen. Three types of nitrogenase exist, the least studied of which is the iron-only nitrogenase. The Anf3 protein in the bacterium Rhodobacter capsulatus is essential for diazotrophic (i.e. nitrogen-fixing) growth with the iron-only nitrogenase, but its enzymatic activity and function are unknown. Here, we biochemically and structurally characterize Anf3 from the model diazotrophic bacterium Azotobacter vinelandii. Determining the Anf3 crystal structure to atomic resolution, we observed that it is a dimeric flavocytochrome with an unusually close interaction between the heme and the flavin adenine dinucleotide cofactors. Measuring the reduction potentials by spectroelectrochemical redox titration, we observed values of -420 ± 10 mV and -330 ± 10 mV for the two FAD potentials and -340 ± 1 mV for the heme. We further show that Anf3 accepts electrons from spinach ferredoxin and that Anf3 consumes oxygen without generating superoxide or hydrogen peroxide. We predict that Anf3 protects the iron-only nitrogenase from oxygen inactivation by functioning as an oxidase in respiratory protection, with flavodoxin or ferredoxin as the physiological electron donors.
Jamshidiha M, Pérez-Dorado I, Murray JW, et al., 2019, Coping with strong translational noncrystallographic symmetry and extreme anisotropy in molecular replacement with Phaser: human Rab27a, Acta Crystallographica Section D Structural Biology, Vol: 75, Pages: 342-353, ISSN: 2059-7983
Data pathologies caused by effects such as diffraction anisotropy and translational noncrystallographic symmetry (tNCS) can dramatically complicate the solution of the crystal structures of macromolecules. Such problems were encountered in determining the structure of a mutant form of Rab27a, a member of the Rab GTPases. Mutant Rab27a constructs that crystallize in the free form were designed for use in the discovery of drugs to reduce primary tumour invasiveness and metastasis. One construct, hRab27a<jats:sup>Mut</jats:sup>, crystallized within 24 h and diffracted to 2.82 Å resolution, with a unit cell possessing room for a large number of protein copies. Initial efforts to solve the structure using molecular replacement by <jats:italic>Phaser</jats:italic> were not successful. Analysis of the data set revealed that the crystals suffered from both extreme anisotropy and strong tNCS. As a result, large numbers of reflections had estimated standard deviations that were much larger than their measured intensities and their expected intensities, revealing problems with the use of such data at the time in <jats:italic>Phaser</jats:italic>. By eliminating extremely weak reflections with the largest combined effects of anisotropy and tNCS, these problems could be avoided, allowing a molecular-replacement solution to be found. The lessons that were learned in solving this structure have guided improvements in the numerical analysis used in <jats:italic>Phaser</jats:italic>, particularly in identifying diffraction measurements that convey very little information content. The calculation of information content could also be applied as an alternative to ellipsoidal truncation. The post-mortem analysis also revealed an oversight in accounting for measurement errors in the fast rotation function. While the crystal of mutant Rab27a is not amenable to drug screening, the structure can guide new modifications to obtain more sui
McFarlane C, Shah N, Kabasakal B, et al., 2018, Structural basis of light-induced redox regulation in the Calvin cycle, biorxiv
Abstract In plants, carbon dioxide is fixed via the Calvin cycle in a tightly regulated process. Key to this regulation is the conditionally disordered protein CP12. CP12 forms a complex with two Calvin cycle enzymes, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK), inhibiting their activities. The mode of CP12 action was unknown. By solving crystal structures of CP12 bound to GAPDH, and the ternary GAPDH-CP12-PRK complex by electron cryo-microscopy, we reveal that formation of the N-terminal disulfide pre-orders CP12 prior to binding the PRK active site. We find that CP12 binding to GAPDH influences substrate accessibility of all GAPDH active sites in the binary and ternary inhibited complexes. Our model explains how CP12 integrates responses from both redox state and nicotinamide dinucleotide availability to regulate carbon fixation. One Sentence Summary How plants turn off carbon fixation in the dark.
Yu J, Knoppova J, Michoux F, et al., 2018, Ycf48 involved in the biogenesis of the oxygen-evolving photosystem II complex is a seven-bladed beta-propeller protein, Proceedings of the National Academy of Sciences, Vol: 115, Pages: E7824-E7833, ISSN: 0027-8424
Robust photosynthesis in chloroplasts and cyanobacteria requires the participation of accessory proteins to facilitate the assembly and maintenance of the photosynthetic apparatus located within the thylakoid membranes. The highly conserved Ycf48 protein acts early in the biogenesis of the oxygen-evolving photosystem II (PSII) complex by binding to newly synthesized precursor D1 subunit and by promoting efficient association with the D2 protein to form a PSII reaction center (PSII RC) assembly intermediate. Ycf48 is also required for efficient replacement of damaged D1 during the repair of PSII. However, the structural features underpinning Ycf48 function remain unclear. Here we show that Ycf48 proteins encoded by the thermophilic cyanobacterium Thermosynechococcus elongatus and the red alga Cyanidioschyzon merolae form seven-bladed beta-propellers with the 19-aa insertion characteristic of eukaryotic Ycf48 located at the junction of blades 3 and 4. Knowledge of these structures has allowed us to identify a conserved “Arg patch” on the surface of Ycf48 that is important for binding of Ycf48 to PSII RCs but also to larger complexes, including trimeric photosystem I (PSI). Reduced accumulation of chlorophyll in the absence of Ycf48 and the association of Ycf48 with PSI provide evidence of a more wide-ranging role for Ycf48 in the biogenesis of the photosynthetic apparatus than previously thought. Copurification of Ycf48 with the cyanobacterial YidC protein insertase supports the involvement of Ycf48 during the cotranslational insertion of chlorophyll-binding apopolypeptides into the membrane.
Krysztofinska EM, Evans NJ, Thapaliya A, et al., 2017, Structure and Interactions of the TPR Domain of Sgt2 with Yeast Chaperones and Ybr137wp., Frontiers in Molecular Biosciences, Vol: 4, ISSN: 2296-889X
Small glutamine-rich tetratricopeptide repeat-containing protein 2 (Sgt2) is a multi-module co-chaperone involved in several protein quality control pathways. The TPR domain of Sgt2 and several other proteins, including SGTA, Hop, and CHIP, is a highly conserved motif known to form transient complexes with molecular chaperones such as Hsp70 and Hsp90. In this work, we present the first high resolution crystal structures of Sgt2_TPR alone and in complex with a C-terminal peptide PTVEEVD from heat shock protein, Ssa1. Using nuclear magnetic resonance spectroscopy and isothermal titration calorimetry, we demonstrate that Sgt2_TPR interacts with peptides corresponding to the C-termini of Ssa1, Hsc82, and Ybr137wp with similar binding modes and affinities.
Beckova M, Yu J, Krynicka V, et al., 2017, Structure of Psb29/Thf1 and its association with the FtsH protease complex involved in photosystem II repair in cyanobacteria, Philosophical Transactions of the Royal Society B: Biological Sciences, Vol: 372, ISSN: 1471-2970
One strategy for enhancing photosynthesis in crop plants is to improve the ability to repair photosystem II (PSII) in response to irreversible damage by light. Despite the pivotal role of thylakoid embedded FtsH protease complexes in the selective degradation of PSII subunits during repair, little is known about the factors involved in regulating FtsH expression. Here we show using the cyanobacterium Synechocystis sp. PCC 6803 that the Psb29 subunit, originally identified as a minor component of His tagged PSII preparations, physically interacts with FtsH complexes in vivo and is required for normal accumulation of the FtsH2/FtsH3 hetero oligomeric complex involved in PSII repair. We show using X ray crystallography that Psb29 from Thermosynechococcus elongatushas a unique fold consisting of a helical bundle and an extended C terminal helix and contains a highly conserved region that might be involved in binding to FtsH. A similar interaction is likely to occur in Arabidopsis chloroplasts between the Psb29 homologue, termed THF1, and the FTSH2/FTSH5 complex. The direct involvement of Psb29/THF1 in FtsH accumulation helps explain why THF1 is a target during the hypersensitive response in plants induced by pathogen infection. Downregulating FtsH function and the PSII repair cycle via THF1 would contribute to the production
Mus F, Eilers BJ, Alleman AB, et al., 2017, Structural Basis for the Mechanism of ATP-Dependent Acetone Carboxylation, SCIENTIFIC REPORTS, Vol: 7, ISSN: 2045-2322
Microorganisms use carboxylase enzymes to form new carbon-carbon bonds by introducing carbon dioxide gas (CO2) or its hydrated form, bicarbonate (HCO3−), into target molecules. Acetone carboxylases (ACs) catalyze the conversion of substrates acetone and HCO3− to form the product acetoacetate. Many bicarbonate-incorporating carboxylases rely on the organic cofactor biotin for the activation of bicarbonate. ACs contain metal ions but not organic cofactors, and use ATP to activate substrates through phosphorylation. How the enzyme coordinates these phosphorylation events and new C-C bond formation in the absence of biotin has remained a mystery since these enzymes were discovered. The first structural rationale for acetone carboxylation is presented here, focusing on the 360 kDa (αβγ)2 heterohexameric AC from Xanthobacter autotrophicus in the ligand-free, AMP-bound, and acetate coordinated states. These structures suggest successive steps in a catalytic cycle revealing that AC undergoes large conformational changes coupled to substrate activation by ATP to perform C-C bond ligation at a distant Mn center. These results illustrate a new chemical strategy for the conversion of CO2 into biomass, a process of great significance to the global carbon cycle.
MacDonald JT, Kabasakal BV, Godding D, et al., 2016, Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension, Proceedings of the National Academy of Sciences of the United States of America, Vol: 113, Pages: 10346-10351, ISSN: 1091-6490
The ability to design and construct structures with atomic level precisionis one of the key goals of nanotechnology. Proteins offer anattractive target for atomic design, as they can be synthesized chemicallyor biologically, and can self-assemble. However the generalizedprotein folding and design problem is unsolved. One approach tosimplifying the problem is to use a repetitive protein as a scaffold.Repeat proteins are intrinsically modular, and their folding and structuresare better understood than large globular domains. Here, wehave developed a new class of synthetic repeat protein, based onthe pentapeptide repeat family of beta-solenoid proteins. We haveconstructed length variants of the basic scaffold, and computationallydesigned de novo loops projecting from the scaffold core. Theexperimentally solved 3.56 ˚A resolution crystal structure of one designedloop matches closely the designed hairpin structure, showingthe computational design of a backbone extension onto a syntheticprotein core without the use of backbone fragments from knownstructures. Two other loop designs were not clearly resolved in thecrystal structures and one loop appeared to be in an incorrect conformation.We have also shown that the repeat unit can accommodatewhole domain insertions by inserting a domain into one of the designedloops.
Rutherford AW, Prell J, MacKellar D, et al., 2016, Streptomyces thermoautotrophicus does not fix nitrogen, Scientific Reports, Vol: 6, ISSN: 2045-2322
Streptomyces thermoautotrophicus UBT1 has been described as a moderately thermophilic chemolithoautotroph with a novel nitrogenase enzyme that is oxygen-insensitive. We have cultured the UBT1 strain, and have isolated two new strains (H1 and P1-2) of very similar phenotypic and genetic characters. These strains show minimal growth on ammonium-free media, and fail to incorporate isotopically labeled N2 gas into biomass in multiple independent assays. The sdn genes previously published as the putative nitrogenase of S. thermoautotrophicus have little similarity to anything found in draft genome sequences, published here, for strains H1 and UBT1, but share >99% nucleotide identity with genes from Hydrogenibacillus schlegelii, a draft genome for which is also presented here. H. schlegelii similarly lacks nitrogenase genes and is a non-diazotroph. We propose reclassification of the species containing strains UBT1, H1, and P1-2 as a non-Streptomycete, non-diazotrophic, facultative chemolithoautotroph and conclude that the existence of the previously proposed oxygen-tolerant nitrogenase is extremely unlikely.
Burgess SJ, Hussein T, Yeoman JA, et al., 2015, Identification of the elusive pyruvate reductase of Chlamydomonas reinhardtii chloroplasts, Plant and Cell Physiology, Vol: 57, Pages: 82-94, ISSN: 1471-9053
Under anoxic conditions the green alga Chlamydomonas reinhardtii activates various 67 fermentation pathways leading to the creation of formate, acetate, ethanol and small 68 amounts of other metabolites including D-lactate and hydrogen. Progress has been 69 made in identifying the enzymes involved in these pathways and their sub-cellular 70 locations; however, the identity of the enzyme involved in reducing pyruvate to D-71 lactate has remained unclear. Based on sequence comparisons, enzyme activity 72 measurements, X-ray crystallography, biochemical fractionation and analysis of 73 knock-down mutants we conclude that pyruvate reduction in the chloroplast is 74 catalysed by a tetrameric NAD⁺-dependent D-lactate dehydrogenase encoded by 75 Cre07.g324550. Its expression during aerobic growth supports a possible function as a 76 ‘lactate valve’ for the export of lactate to the mitochondrion for oxidation by 77 cytochrome-dependent D-lactate dehydrogenases and by glycolate dehydrogenase. 78 We also present a revised spatial model of fermentation based on our 79 immunochemical detection of the likely pyruvate decarboxylase, PDC3, in the 80 cytoplasm.
Cotton CAR, Kabasakal BV, Miah N, et al., 2015, Structure of the dual-function fructose-1,6/sedoheptulose-1,7-bisphosphatase from Thermosynechococcus elongatus bound with sedoheptulose-7-phosphate, Acta Crystallographica Section F, Vol: F71, Pages: 1341-1345, ISSN: 2053-230X
The dual-function fructose-1,6/sedoheptulose-1,7-bisphosphatase (FBP/SBPase) in cyanobacteria carries out two activities in the Calvin cycle. Structures of this enzyme from the cyanobacterium Synechocystis sp. PCC 6803 exist, but only with adenosine monophosphate (AMP) or fructose-1,6-bisphosphate and AMP bound. The mechanisms which control both selectivity between the two sugars and the structural mechanisms for redox control are still unresolved. Here, the structure of the dual-function FBP/SBPase from the thermophilic cyanobacterium Thermosynechococcus elongatus is presented with sedoheptulose-7-phosphate bound and in the absence of AMP. The structure is globally very similar to the Synechocystis sp. PCC 6803 enzyme, but highlights features of selectivity at the active site and loop ordering at the AMP-binding site. Understanding the selectivity and control of this enzyme is critical for understanding the Calvin cycle in cyanobacteria and for possible biotechnological application in plants.
Cardona Londono T, Murray JW, Rutherford AW, 2015, Origin and evolution of water oxidation before the last common ancestor of the Cyanobacteria, Molecular Biology and Evolution, ISSN: 1537-1719
Photosystem II, the water oxidizing enzyme, altered the course of evolution by filling the atmosphere with oxygen. Here, we reconstruct the origin and evolution of water oxidation at an unprecedented level of detail by studying the phylogeny of all D1 subunits, the main protein coordinating the water oxidizing cluster (Mn4CaO5) of Photosystem II. We show that D1 exists in several forms making well-defined clades, some of which could have evolved before the origin of water oxidation and presenting many atypical characteristics. The most ancient form is found in the genome of Gloeobacter kilaueensis JS-1 and this has a C-terminus with a higher sequence identity to D2 than to any other D1. Two other groups of early evolving D1 correspond to those expressed under prolonged far-red illumination and in darkness. These atypical D1 forms are characterized by a dramatically different Mn4CaO5 binding site and a Photosystem II containing such a site may assemble an unconventional metal cluster. The first D1 forms with a full set of ligands to the Mn4CaO5 cluster are grouped with D1 proteins expressed only under low oxygen concentrations and the latest evolving form is the dominant type of D1 found in all cyanobacteria and plastids. In addition, we show that the plastid ancestor had a D1 more similar to those in early branching Synechococcus. We suggest each one of these forms of D1 originated from transitional forms at different stages towards the innovation and optimization of water oxidation before the last common ancestor of all known cyanobacteria.
Kabasakal BV, Kabasakal BV, Cotton C, et al., 2015, Structural insights into malonyl-CoA reductase of 3-hydroxypropionate cycle, Publisher: INT UNION CRYSTALLOGRAPHY, Pages: S202-S202, ISSN: 2053-2733
Hingorani K, Pace R, Whitney S, et al., 2014, Photo-oxidation of tyrosine in a bio-engineered bacterioferritin 'reaction centre'-A protein model for artificial photosynthesis, BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, Vol: 1837, Pages: 1821-1834, ISSN: 0005-2728
Michoux F, Boehm M, Bialek W, et al., 2014, Crystal structure of CyanoQ from the thermophilic cyanobacterium Thermosynechococcus elongatus and detection in isolated photosystem II complexes, PHOTOSYNTHESIS RESEARCH, Vol: 122, Pages: 57-67, ISSN: 0166-8595
Murray JW, 2014, Protein design for artificial photosynthesis, 247th National Spring Meeting of the American-Chemical-Society (ACS), Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Bialek W, Wen S, Michoux F, et al., 2013, Crystal structure of the Psb28 accessory factor of Thermosynechococcus elongatus photosystem II at 2.3 angstrom, PHOTOSYNTHESIS RESEARCH, Vol: 117, Pages: 375-383, ISSN: 0166-8595
Murray JW, 2013, Light and Life Photosynthesis, Biochemist, Vol: 35, Pages: 4-7, ISSN: 0954-982X
Complex life on Earth requires oxygen as the terminal electron acceptor in the respiratory chain. However, the lifetime of a single oxygen molecule in the atmosphere is only 4500 years. Oxygen is continually being replenished by the action of photosynthetic organisms, using the only substantial energy input to the Earth, sunlight. How this light energy is harvested and used is of fundamental biological importance, and may be of crucial importance in developing sustainable energy technologies. © Biochemical Society.
Canning P, Cooper CDO, Krojer T, et al., 2013, Structural basis for Cul3 protein assembly with the BTB-Kelch family of E3 ubiquitin ligases (vol 288, pg 7803, 2013), JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 288, Pages: 28304-28304
Moore BL, Kelley LA, Barber J, et al., 2013, High-quality protein backbone reconstruction from alpha carbons using gaussian mixture models, JOURNAL OF COMPUTATIONAL CHEMISTRY, Vol: 34, Pages: 1881-1889, ISSN: 0192-8651
Canning P, Cooper CDO, Krojer T, et al., 2013, Structural Basis for Cul3 Protein Assembly with the BTB-Kelch Family of E3 Ubiquitin Ligases, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 288, Pages: 7803-7814
Simon AC, Simpson PJ, Goldstone RM, et al., 2013, Structure of the Sgt2/Get5 complex provides insights into GET-mediated targeting of tail-anchored membrane proteins, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 110, Pages: 1327-1332, ISSN: 0027-8424
Michoux F, Takasaka K, Boehm M, et al., 2012, Crystal structure of the Psb27 assembly factor at 1.6: implications for binding to Photosystem II, PHOTOSYNTHESIS RESEARCH, Vol: 110, Pages: 169-175, ISSN: 0166-8595
Murray JW, 2012, Sequence variation at the oxygen-evolving centre of photosystem II: a new class of 'rogue' cyanobacterial D1 proteins, PHOTOSYNTHESIS RESEARCH, Vol: 110, Pages: 177-184, ISSN: 0166-8595
Murray J, 2012, Redox active protein maquettes: Multi-functional"green enzymes", RSC Energy and Environment Series, Vol: 2012, Pages: 408-425, ISSN: 2044-0774
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