Staff Publications

Staff Publications

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    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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Lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system
Desguin, B. ; Goffin, P. ; Viaene, E. ; Kleerebezem, M. ; Martin-Diaconescu, V. ; Maroney, M.J. ; Declercq, J.P. ; Soumillion, P. ; Hols, P. - \ 2014
Nature Communications 5 (2014). - ISSN 2041-1723
lactobacillus-plantarum - lactic-acid - racemization - binding - dehydrogenase - purification - proteins - bacteria - growth - model
Racemases catalyse the inversion of stereochemistry in biological molecules, giving the organism the ability to use both isomers. Among them, lactate racemase remains unexplored due to its intrinsic instability and lack of molecular characterization. Here we determine the genetic basis of lactate racemization in Lactobacillus plantarum. We show that, unexpectedly, the racemase is a nickel-dependent enzyme with a novel a/ß fold. In addition, we decipher the process leading to an active enzyme, which involves the activation of the apo-enzyme by a single nickel-containing maturation protein that requires preactivation by two other accessory proteins. Genomic investigations reveal the wide distribution of the lactate racemase system among prokaryotes, showing the high significance of both lactate enantiomers in carbon metabolism. The even broader distribution of the nickel-based maturation system suggests a function beyond activation of the lactate racemase and possibly linked with other undiscovered nickel-dependent enzymes.
Protective effect of Phellinus linteus polysaccharide extracts against thioacetamide-induced liver fibrosis in rats: a proteomics analysis
Wang, H. ; Wu, G. ; Park, H.J. ; Jiang, P.P. ; Sit, W.H. ; Griensven, L.J.L.D. van; Wan, J.M.F. - \ 2012
Chinese Medicine 7 (2012). - ISSN 1749-8546
hepatocellular-carcinoma - oxidative stress - chain - injury - mice - gene - methyltransferase - differentiation - dehydrogenase - metastasis
Background: The hepatoprotective potential of Phellinus linteus polysaccharide (PLP) extracts has been described. However, the molecular mechanism of PLP for the inhibition of liver fibrosis is unclear. This study aims to investigate the molecular protein signatures involved in the hepatoprotective mechanisms of PLP via a proteomics approach using a thioacetamide (TAA)-induced liver fibrosis rat model. Methods: Male Sprague-Dawley rats were divided into three groups of six as follows: Normal group; TAA group, in which rats received TAA only; and PLP group, in which rats received PLP and TAA. Liver fibrosis was induced in the rats by repeated intraperitoneal injections of TAA at a dose of 200 mg/kg body weight twice a week for 4 weeks. PLP was given orally at a dose of 50 mg/kg body weight twice a day from the beginning of the TAA treatment until the end of the experiment. The development of liver cirrhosis was verified by histological examination. Liver proteomes were established by two-dimensional gel electrophoresis. Proteins with significantly altered expression levels were identified by matrix-assisted laser desorption/ionization-time of flight/time of flight mass spectrometry and the differentially expressed proteins were validated by immunohistochemical staining and reverse transcription polymerase chain reaction. Results: Histological staining showed a remarkable reduction in liver fibrosis in the rats with PLP treatment. A total of 13 differentially expressed proteins including actin, tubulin alpha-1C chain, preprohaptoglobin, hemopexin, galectin-5, glutathione S-transferase alpha-4 (GSTA4), branched chain keto acid dehydrogenase hterotetrameric E1 subunit alpha (BCKDHA), glutathione S-transferase mu (GSTmu); glyceraldehyde-3-phosphate dehydrogenase (GAPDH); thiosulfate sulfurtransferase (TFT); betaine-homocysteine S-methyltransferase 1 (BHMT1); quinoid dihydropteridine reductase (QDPR); ribonuclease UK114 were observed between the TAA and PLP groups. These proteins are involved in oxidative stress, heme and iron metabolism, cysteine metabolism, and branched-chain amino acid catabolism. Conclusion: The proteomics data indicate that P. linteus may be protective against TAA-induced liver fibrosis via regulation of oxidative stress pathways, heat shock pathways, and metabolic pathways for amino acids and nucleic acids.
Comparatiave analysis of the grain proteome fraction in barley genotypes with contrasting salinity tolerance during germination
Witzel, K. ; Weidner, A. ; Surabhi, G.K. ; Varshney, R.K. ; Kunze, G. ; Buck-Sorlin, G.H. ; Börner, A. ; Mock, H.P. - \ 2010
Plant, Cell & Environment 33 (2010)2. - ISSN 0140-7791 - p. 211 - 222.
abiotic stress-response - quantitative trait loci - salt tolerance - osmotic-stress - comparative transcriptome - heading date - dehydrogenase - gene - rice - resistance
In the present paper, we based a search for candidates underlying different levels of salinity tolerance during germination in the Oregon Wolfe Barley mapping population (DOM × REC) by proteomic profiling of the mature grain of lines showing differing levels of salinity tolerance. By contrasting the parents DOM and REC, displaying divergent stress responses, and two tolerant and two sensitive segregants, six protein spots were identified that showed a differential abundance between the tolerant and the sensitive lines. The tolerant lines expressed a higher level of 6-phosphogluconate dehydrogenase and glucose/ribitol dehydrogenase (Glc/RibDH). Both proteins were heterologously over-expressed in an osmo-sensitive yeast strain and over-expression of Glc/RibDH resulted in an enhanced ability of yeast transformants to grow on salt containing media. A quantitative trait locus (QTL) analysis of the population germinating at different salt concentrations led to the identification of two chromosome regions on 5H and one on 7H associated with salt stress response. A dense barley transcript map was employed to map the genomic region of all identified proteins. Two of these, heat-shock protein 70 and Glc/RibDH, co-localized with the identified QTL on chromosome 5H. The putative functional role of the candidates is discussed
SulfoSYS (Sulfolobus Systems Biology): towards a silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation
Albers, S.V. ; Birkeland, N.K. ; Driessen, A.J.M. ; Gertig, S. ; Haferkamp, P. ; Klenk, H.P. ; Kouril, T. ; Manica, A. ; Pham, T.K. ; Ruoff, P. ; Schleper, C. ; Schomburg, D. ; Sharkey, K. ; Siebers, B. ; Sierocinski, P. ; Steur, R. ; Oost, J. van der; Westerhoff, H.V. ; Wieloch, P. ; Wright, P.C. ; Zaparty, M. - \ 2009
Biochemical Society Transactions 37 (2009)1. - ISSN 0300-5127 - p. 58 - 64.
entner-doudoroff pathway - dna microarray analysis - thermoproteus-tenax - key-enzyme - promiscuity - gene - identification - dehydrogenase - dehydratase - disruption
SulfoSYS (Sulfolobus Systems Biology) focuses on the study of the CCM (central carbohydrate metabolism) of Sulfolobus solfataricus and its regulation under temperature variation at the systems level. In Archaea, carbohydrates are metabolized by modifications of the classical pathways known from Bacteria or Eukarya, e.g. the unusual branched ED (Entner-Doudoroff) pathway, which is utilized for glucose degradation in S. solfataricus. This archaeal model organism of choice is a thermoacidophilic crenarchaeon that optimally grows at 80 degrees C (60-92 degrees C) and pH 2-4. In general, life at high temperature requires very efficient adaptation to temperature changes, which is most difficult to deal with for organisms, and it is unclear how biological networks can withstand and respond to such changes. This integrative project combines genomic, transcriptomic, proteomic and metabolomic, as well as kinetic and biochemical information. The final goal of SulfoSYS is the construction of a silicon cell model for this part of the living cell that will enable computation of the CCM network. In the present paper, we report on one of the first archaeal systems biology projects
Reversible interconversion of carbon dioxide and formate by an electroactive enzyme
Reda, T. ; Plugge, C.M. ; Abram, N.J. ; Hirst, J. - \ 2008
Proceedings of the National Academy of Sciences of the United States of America 105 (2008)31. - ISSN 0027-8424 - p. 10654 - 10658.
crystal-structure - syntrophobacter-fumaroxidans - dehydrogenase - tungsten - co2 - molybdenum - reduction - catalysis - selenocysteine - molybdopterin
Carbon dioxide (CO2) is a kinetically and thermodynamically stable molecule. It is easily formed by the oxidation of organic molecules, during combustion or respiration, but is difficult to reduce. The production of reduced carbon compounds from CO2 is an attractive proposition, because carbon-neutral energy sources could be used to generate fuel resources and sequester CO2 from the atmosphere. However, available methods for the electrochemical reduction of CO2 require excessive overpotentials (are energetically wasteful) and produce mixtures of products. Here, we show that a tungsten-containing formate dehydrogenase enzyme (FDH1) adsorbed to an electrode surface catalyzes the efficient electrochemical reduction of CO2 to formate. Electrocatalysis by FDH1 is thermodynamically reversible¿only small overpotentials are required, and the point of zero net catalytic current defines the reduction potential. It occurs under thoroughly mild conditions, and formate is the only product. Both as a homogeneous catalyst and on the electrode, FDH1 catalyzes CO2 reduction with a rate more than two orders of magnitude faster than that of any known catalyst for the same reaction. Formate oxidation is more than five times faster than CO2 reduction. Thermodynamically, formate and hydrogen are oxidized at similar potentials, so formate is a viable energy source in its own right as well as an industrially important feedstock and a stable intermediate in the conversion of CO2 to methanol and methane. FDH1 demonstrates the feasibility of interconverting CO2 and formate electrochemically, and it is a template for the development of robust synthetic catalysts suitable for practical applications
Biodegradation pathway of L-glutamatediacetate by Rhizobium radiobacter strain BG-1
Ginkel, C.G. van; Geerts, R. ; Nguyen, P.D. ; Plugge, C.M. - \ 2008
International Biodeterioration and Biodegradation 62 (2008)1. - ISSN 0964-8305 - p. 31 - 37.
chelatobacter-heintzii - agrobacterium sp - edta - degradation - iminodisuccinate - purification - identification - stereoisomers - dehydrogenase - bacterium
An aerobic bacterium was isolated from activated sludge in a medium containing l-glutamate-N,N-diacetate (l-GLDA) as sole carbon and energy source. The isolate was identified as a Rhizobium radiobacter species. Besides l-GLDA, the strain utilized nitrilotriacetate (NTA) and proposed intermediates in l-GLDA metabolism such as glyoxylate and l-glutamate. l-GLDA-grown cells oxidized l-GLDA, l-glutamate but not iminodiacetate (IDA), and trans-ketoglutaconate, indicating removal of a carboxymethyl group as an initial degradation reaction. The removal of the first carboxymethyl group of l-GLDA is catalyzed by an NADH-dependent mono-oxygenase. The oxidative deamination of l-glutamate by a dehydrogenase resulting in the formation of oxoglutarate was also detected in cell-free extracts of R. radiobacter sp. A pathway for the metabolism of l-GLDA R. radiobacter sp. is proposed: First, l-GLDA leads to l-glutamate-N-monoacetate (l-GLMA) which in turn leads to l-glutamate. Then, l-glutamate leads to oxoglutarate, an intermediate of the TCA cycle.
Bootstrapping the energy flow in the beginning of life
Hengeveld, R. ; Fedonkin, M.A. - \ 2007
Acta Biotheoretica 55 (2007)2. - ISSN 0001-5342 - p. 181 - 226.
evolution - hydrogen - enzymes - nickel - dehydrogenase - hypothesis - redox - earth
This paper suggests that the energy flow on which all living structures depend only started up slowly, the low-energy, initial phase starting up a second, slightly more energetic phase, and so on. In this way, the build up of the energy flow follows a bootstrapping process similar to that found in the development of computers, the first generation making possible the calculations necessary for constructing the second one, etc. In the biogenetic upstart of an energy flow, non-metals in the lower periods of the Periodic Table of Elements would have constituted the most primitive systems, their operation being enhanced and later supplanted by elements in the higher periods that demand more energy. This bootstrapping process would put the development of the metabolisms based on the second period elements carbon, nitrogen and oxygen at the end of the evolutionary process rather than at, or even before, the biogenetic event
Two approaches to the study of the origin of life
Hengeveld, R. - \ 2007
Acta Biotheoretica 55 (2007)2. - ISSN 0001-5342 - p. 97 - 131.
atmospheric oxygen - evolution - enzymes - redox - phosphorylation - photosynthesis - dehydrogenase - chloroplasts - metabolism - hypothesis
This paper compares two approaches that attempt to explain the origin of life, or biogenesis. The more established approach is one based on chemical principles, whereas a new, yet not widely known approach begins from a physical perspective. According to the first approach, life would have begun with - often organic - compounds. After having developed to a certain level of complexity and mutual dependence within a non-compartmentalised organic soup, they would have assembled into a functioning cell. In contrast, the second, physical type of approach has life developing within tiny compartments from the beginning. It emphasises the importance of redox reactions between inorganic elements and compounds found on two sides of a compartmental boundary. Without this boundary, ¿life¿ would not have begun, nor have been maintained; this boundary - and the complex cell membrane that evolved from it - forms the essence of life.
Kinetically controlled refolding of a heat denatured hyperthermostable protein
Koutsopoulos, S. ; Oost, J. van der; Norde, W. - \ 2007
FEBS Journal 274 (2007)22. - ISSN 1742-464X - p. 5915 - 5923.
archaeon pyrococcus-furiosus - crystal-structure - thermodynamic properties - thermal-denaturation - citrate synthase - stability - temperature - enzyme - water - dehydrogenase
The thermal denaturation of endo-ß-1,3-glucanase from the hyperthermophilic microorganism Pyrococcus furiosus was studied by calorimetry. The calorimetric profile revealed two transitions at 109 and 144¿°C, corresponding to protein denaturation and complete unfolding, respectively, as shown by circular dichroism and fluorescence spectroscopy data. Calorimetric studies also showed that the denatured state did not refold to the native state unless the cooling temperature rate was very slow. Furthermore, previously denatured protein samples gave well-resolved denaturation transition peaks and showed enzymatic activity after 3 and 9¿months of storage, indicating slow refolding to the native conformation over time.
Dihydrodipicolinate synthase in opaque and floury maize mutants
Varisi, V.A. ; Medici, L.O. ; Meer, I.M. van der; Lea, P.J. ; Azevedo, J.L. - \ 2007
Plant Science 173 (2007)4. - ISSN 0168-9452 - p. 458 - 467.
endosperm protein-synthesis - lysine metabolism - higher-plants - aspartate kinase - s-adenosylmethionine - sorghum seeds - rice seeds - dehydrogenase - biosynthesis - catabolism
Dihydrodipicolinate synthase (DHDPS, EC was isolated and studied in four high-lysine maize mutants (Oh43o1, Oh43o2, Oh43fl1 and Oh43fl2). The activity of DHDPS was analyzed at 16, 20, and 24 DAP and characterized in the presence of the amino acids, lysine, S-(2-aminoethyl)-l-cysteine (AEC), S-adenosylmethionine (SAM) and calcium. The results indicated that DHDPS was strongly inhibited by lysine, and that there was little variation between the mutants, indicating that lysine accumulation in these mutants may be more dependent on other enzymes involved in lysine metabolism. The higher concentrations of lysine observed in the seeds of the mutants at maturity may be explained by the accumulation of soluble lysine caused by a reduction in lysine degradation, or by changes in the distribution of high lysine containing storage proteins.
Transcription profiling of the metal-hyperaccumulator Thlaspi caerulescens
Plessi, M. ; Rigola, D. ; Hassinen, V. ; Aarts, M.G.M. ; Schat, H. ; Ernst, D. - \ 2005
Zeitschrift für Naturforschung. Section C : a Journal of Biosciences 60 (2005)3-4. - ISSN 0939-5075 - p. 216 - 223.
arabidopsis-halleri - microarray analysis - gene-expression - accumulation - populations - plants - dehydrogenase - transporter - tolerance - reveals
Thlaspi caerulescens is a well-studied metal-hyperaccumulator of zinc, cadmium and nickel, belonging to the Brassicaceae family. Moreover it is one of the few hyperaccumulators that occur on different metalliferous soil types, as well as on nonmetalliferous soils. We are interested in the development of systems to improve phytoremediation of metal contaminated soils through improved metal-accumulation. About 1900 cDNAs isolated from T. caerulescens roots were hybridized with reverse transcribed RNA from zinc-treated T. caerulescens plants of two accessions originating from two different soil types. This comparative transcript profiling of T. caerulescens plants resulted in the identification of genes that are affected by heavy metals. The developed microarray proved to be an appropriate tool for a large scale analysis of gene expression in this metal-accumulator species.
Promoter rearrangements cause species-specific hepatic regulation of the glyoxylate reductase/hydroxypyruvate reductase gene by the peroxisome proliferator-activated receptor a
Genolet, R. ; Kersten, A.H. ; Braissant, O. ; Mandard, S.J. ; Tan, N.S. ; Bucher, P. ; Desvergne, B. ; Michalik, L. ; Wahli, W. - \ 2005
Journal of Biological Chemistry 280 (2005)25. - ISSN 0021-9258 - p. 24143 - 24152.
urinary oxalate - alpha - hyperoxaluria - dehydrogenase - metabolism - complex - protein - rats
In liver, the glyoxylate cycle contributes to two metabolic functions, urea and glucose synthesis. One of the key enzymes in this pathway is glyoxylate reductase/hydroxypyruvate reductase (GRHPR) whose dysfunction in human causes primary hyperoxaluria type 2, a disease resulting in oxalate accumulation and formation of kidney stones. In this study, we provide evidence for a transcriptional regulation by the peroxisome proliferator-activated receptor (PPAR) of the mouse GRHPR gene in liver. Mice fed with a PPAR ligand or in which PPAR activity is enhanced by fasting increase their GRHPR gene expression via a peroxisome proliferator response element located in the promoter region of the gene. Consistent with these observations, mice deficient in PPAR present higher plasma levels of oxalate in comparison with their wild type counterparts. As expected, the administration of a PPAR ligand (Wy-14,643) reduces the plasma oxalate levels. Surprisingly, this effect is also observed in null mice, suggesting a PPAR-independent action of the compound. Despite a high degree of similarity between the transcribed region of the human and mouse GRHPR gene, the human promoter has been dramatically reorganized, which has resulted in a loss of PPAR regulation. Overall, these data indicate a species-specific regulation by PPAR of GRHPR, a key gene of the glyoxylate cycle.
Temperature-dependent structural and functional features of a hyperthermostable enzyme using elastic neutron scattering
Koutsopoulos, S. ; Oost, J. van der; Norde, W. - \ 2005
Proteins : Structure, Function, and Bioinformatics 61 (2005)2. - ISSN 0887-3585 - p. 377 - 384.
archaeon pyrococcus-furiosus - crystal-structure - protein dynamics - 2.5-angstrom resolution - angstrom resolution - citrate synthase - thermostability - dehydrogenase - stability - fluctuations
The dynamic behavior of an endoglucanase from the hyperthermophilic microorganism Pyrococcus furiosus was investigated using elastic neutron scattering. The temperature dependence of the atomic motions was correlated with conformational and functional characteristics of the enzyme. The onset of biological function at temperatures higher than approximately 25°C (the hyperthermostable enzyme is essentially inactive at room temperature) was associated with a dynamical transition in the anharmonic motions domain. This transition from the nonactive to the enzymatically active conformation involved structurally similar conformational substates in the energy landscape. From the mean-square displacement of the protein atoms, the molecular flexibility and the effective force constants were calculated at different temperature zones. The results showed that the activity increases at higher temperatures where the intramolecular bonds are weakened and the overall rigidity of the protein is decreased. Further temperature increase resulted in significantly increased atomic fluctuations featuring heat denaturation of the protein
Degradation pathway of 2-chloroethanol in Pseudomonas stutzeri strain JJ under denitrifying conditions
Dijk, J.A. ; Gerritse, J. ; Schraa, G. ; Stams, A.J.M. - \ 2004
Archives of Microbiology 182 (2004)6. - ISSN 0302-8933 - p. 514 - 519.
vinyl-chloride - pyrroloquinoline quinone - dehydrogenase - metabolism - pqq - mineralization - chloroethanol - intermediate - oxidation - aquifer
The pathway of 2-chloroethanol degradation in the denitrifying Pseudomonas stutzeri strain JJ was investigated. In cell-free extracts, activities of a phenazine methosulfate (PMS)-dependent chloroethanol dehydrogenase, an NAD-dependent chloroacetaldehyde dehydrogenase, and a chloroacetate dehalogenase were detected. This suggested that the 2-chloroethanol degradation pathway in this denitrifying strain is the same as found in aerobic bacteria that degrade chloroethanol. Activity towards primary alcohols, secondary alcohols, diols, and other chlorinated alcohols could be measured in cell-free extracts with chloroethanol dehydrogenase (CE-DH) activity. PMS and phenazine ethosulfate (PES) were used as primary electron acceptors, but not NAD, NADP or ferricyanide. Cells of strain JJ cultured in a continuous culture under nitrate limitation exhibited chloroethanol dehydrogenase activity that was a 12 times higher than in cells grown in batch culture. However, under chloroethanol-limiting conditions, CE-DH activity was in the same range as in batch culture. Cells grown on ethanol did not exhibit CE-DH activity. Instead, NAD-dependent ethanol dehydrogenase (E-DH) activity and PMS-dependent E-DH activity were detected
Biocatalytic potential of p-hydroxybenzoate hydroxylase from Rhodococcus rhodnii 135 and Rhodococcus opacus 557
Jadan, A.P. ; Moonen, M.J.H. ; Golovleva, L.A. ; Rietjens, I.M.C.M. ; Berkel, W.J.H. van - \ 2004
Advanced Synthesis and Catalysis 346 (2004)2-3. - ISSN 1615-4150 - p. 367 - 375.
wild-type - flavin - erythropolis - purification - substrate - monooxygenase - dehydrogenase - activation - mechanism - binding
The biocatalytic potential of the NADH-dependent p-hydroxybenzoate hydroxylases (PHBH) from Rhodococcus rhodnii 135 and Rhodococcus opacus 557 was investigated. Monofluorinated 4-hydroxybenzoates were efficiently hydroxylated, albeit at different rates. 2-Fluoro-4-hydroxybenzoate was a true substrate for PHBH from R. rhodnii 135 but a substrate inhibitor for PHBH from R. opacus 557. Monochlorinated 4-hydroxybenzoates also acted as PHBH substrates, but with these compounds strong uncoupling of hydroxylation (formation of hydrogen peroxide) occurred. PHBH from R. rhodnii 135 preferred the 5'-hydroxylation of 2-chloro-4-hydroxybenzoate but the enzyme from R. opacus 557 favored the formation of 2-chloro-3,4-dihydroxybenzoate. Conversely, PHBH from R. rhodnii 135 regioselectively hydroxylated 2-fluoro-4-hydroxybenzoate to 2-fluoro-3,4-dihydroxybenzoate whereas the enzyme from R. opacus 557 also produced significant amounts of 2-fluoro-4,5-dihydroxybenzoate. At high NADH/substrate ratio, both 2-fluorodihydroxybenzoate products were further converted to 2-fluoro3,4,5-trihydroxybenzoate. PHBH from R. rhodnii 135 and R. opacus 557 preferred the 5'-hydroxylation of 3-chloro-4-hydroxybenzoate. However, conversion of 3-fluoro-4-hydroxybenzoate involved considerable dehalogenation affording nearly equal amounts of 3,4-dihydroxybenzoate and 5-fluoro-3,4-dihydroxybenzoate. At high NADH/substrate ratio, the latter compound was further converted to 3,4,5-trihydroxybenzoate. The results are discussed in relation to the properties of the NADPH-specific PHBH from Pseudomonas fluorescens.
Characterization of the chlorate reductase from Pseudomonas chloritidismutans
Wolterink, A.F.W.M. ; Schiltz, E. ; Hagedoorn, P.L. ; Hagen, W.R. ; Kengen, S.W.M. ; Stams, A.J.M. - \ 2003
Journal of Bacteriology 185 (2003)10. - ISSN 0021-9193 - p. 3210 - 3213.
desulfovibrio-vulgaris hildenborough - nitrate reductase - paracoccus-denitrificans - haloarcula-marismortui - energy transduction - oxide reductase - purification - dehydrogenase - (per)chlorate - enzymes
A chlorate reductase has been purified from the chlorate-reducing strain Pseudomonas chloritidismutans. Comparison with the periplasmic (per)chlorate reductase of strain GR-1 showed that the cytoplasmic chlorate reductase of P. chloritidismutans reduced only chlorate and bromate. Differences were also found in N-terminal sequences, molecular weight, and subunit composition. Metal analysis and electron paramagnetic resonance measurements showed the presence of iron and molybdenum, which are also found in other dissimilatory oxyanion reductases
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