Modeling the structure of <i>pyrococcus furiosus</i> rubredoxin by homology to other X‐ray structures

Wampler, John E.; Bradley, Elizabeth A.; Adams, Michael W. W.; Stewart, David E.

doi:10.1002/pro.5560020414

Cited by 15 publications

(4 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Heme labels are ordered from the N-terminus. Following the same homology modeling procedures previously described (Stewart et al, 1987;Wampler et al, 1993), the predicted structure of the D. desulfuricans ATCC 27774 cytochrome c3 presents a high similarity to the X-ray structure of the parent protein from D. vulgaris Miyazaki F. This result is not surprising, since the two molecules have the same number of amino acids and a significant degree of homology (40%), and the minimization process used will not change conformations dramatically, in any case. Since the relative position and orientation of these four hemes are strongly conserved among the known structures, it seems reasonable to form the homology model by such a procedure.…”

Section: U_imentioning

confidence: 78%

Evidence for a Ternary Complex Formed between Flavodoxin and Cytochrome c3: 1H-NMR and Molecular Modeling Studies

Palma

Moura

LeGall³

et al. 1994

Biochemistry

Self Cite

View full text Add to dashboard Cite

Small electron-transfer proteins such as flavodoxin (16 kDa) and the tetraheme cytochrome c3 (13 kDa) have been used to mimic, in vitro, part of the complex electron-transfer chain operating between substrate electron donors and respiratory electron acceptors, in sulfate-reducing bacteria (Desulfovibrio species). The nature and properties of the complex formed between these proteins are revealed by 1H-NMR and molecular modeling approaches. Our previous study with the Desulfovibrio vulgaris proteins [Moura, I., Moura, J.J. G., Santos, M.H., & Xavier, A. V. (1980) Cienc. Biol. (Portugal) 5, 195-197; Stewart, D.E. LeGall, J., Moura, I., Moura, J. J. G., Peck, H.D. Jr., Xavier, A. V., Weiner, P. K., & Wampler, J.E. (1988) Biochemistry 27, 2444-2450] indicated that the complex between cytochrome c3 and flavodoxin could be monitored by changes in the NMR signals of the heme methyl groups of the cytochrome and that the electrostatic surface charge (Coulomb's law) on the two proteins favored interaction between one unique heme of the cytochrome with flavodoxin. If the interaction is indeed driven by the electrostatic complementarity between the acidic flavodoxin and a unique positive region of the cytochrome c3, other homologous proteins from these two families of proteins might be expected to interact similarly. In this study, three homologous Desulfovibrio cytochromes c3 were used, which show a remarkable variation in their individual isoelectric points (ranging from 5.5 to 9.5). On the basis of data obtained from protein-protein titrations followed at specific proton NMR signals (i.e., heme methyl resonances), a binding model for this complex has been developed with evaluation of stoichiometry and binding constants. This binding model involves one site on the cytochromes c3 and two sites on the flavodoxin, with formation of a ternary complex at saturation. In order to understand the potential chemical form of the binding model, a structural model for the hypothetical ternary complex, formed between one molecule of Desulfovibrio salexigens flavodoxin and two molecules of cytochrome c3, is proposed. These molecular models of the complexes were constructed on the basis of complementarity of Coulombic electrostatic surface potentials, using the available X-ray structures of the isolated proteins and, when required, model structures (D. salexigens flavodoxin and Desulfovibrio desulfuricans ATCC 27774 cytochrome c3) predicted by homology modeling.

show abstract

Section: U_imentioning

confidence: 78%

Evidence for a Ternary Complex Formed between Flavodoxin and Cytochrome c3: 1H-NMR and Molecular Modeling Studies

Palma

Moura

LeGall³

et al. 1994

Biochemistry

Self Cite

View full text Add to dashboard Cite

show abstract

“…The function of this small (M r = 5500) iron-containing redox protein has yet to be established [8,57] so a role in S ° reduction is an intriguing possibility. This protein is also of some interest as it is the first hyperthermophilic protein for which a three-dimensional structure is available [95][96][97]. It was also demonstrated [94] that S ° reduction appears to be a general property of some, if not all, hydrogenases, hence the primary or even sole function of an ancestral hydrogenase may have been to reduce S ° (or polysulfide).…”

Section: Mechanisms Of S ° Reduction By P Furiosusmentioning

confidence: 98%

Biochemical diversity among sulfur-dependent, hyperthermophilic microorganisms

Adams

1994

FEMS Microbiology Reviews

View full text Add to dashboard Cite

Hyperthermophiles are a recently discovered group of microorganisms that grow at and above 90°C. They currently comprise over 20 different genera, and except for two novel bacleria, all are classified as Archaea. The majority of these organisms are obligately anaerobic heterotrophs that reduce elemental sulfur (S °) to H2S. The best studied from a biochemical perspective are the archaeon, ~'rococcus furiosus, and the bacterium, Thermotoga rnaritirna, both of which are saccharolytic. P. furiosus is thought to contain a new type of Entner-Doudoroff pathway for the conversion of carbohydrates ultimately to acetate, H 2 and CO~. The pathway is independent of nicotinamide nucleotides and involves novel types of ferredoxin-linked oxidoreductases, one of which has tungsten, a rarely used element, as a prosthetic group. The only site of energy conservation is at the level of acetyl CoA, which in the presence of ADP and phosphate is converted to acetate and ATP in a single step. In contrast, 72 maritima utilizes a conventional Embden-Meyerhof pathway for sugar oxidation. P. furiosus also utilizes peptides as a sole carbon and energy source. Amino acid oxidation is thought to involve glutamate dehydrogenase together with at least three types of novel ferredoxin-linked oxidoreductases which catalyze the oxidation of 2-ketoglutarate, aryl pyruvates and formaldehyde. One of these enzymes also utilizes tungsten. In P. furiosus, virtually all of the reductant that is generated during the catabolism of both carbohydrates and peptides is channeled to a cytoplasmic hydrogenase. This enzyme is now termed sulhydrogenase, as it reduces both protons to H 2 and S ° (or polysulfide) to H2S. S ° reduction appears to lead to the conservation of energy in P. furiosus but not in 72 rnaritima, although the mechanism by which this occurs is not known.

show abstract

Section: Mechanisms Of S ° Reduction By P Furiosusmentioning

confidence: 99%

Biochemical diversity among sulfur-dependent, hyperthermophilic microorganisms

Adams

1994

FEMS Microbiology Reviews

Self Cite

View full text Add to dashboard Cite

Hyperthermophiles are a recently discovered group of microorganisms that grow at and above 90 degrees C. They currently comprise over 20 different genera, and except for two novel bacteria, all are classified as Archaea. The majority of these organisms are obligately anaerobic heterotrophs that reduce elemental sulfur (S degree) to H2S. The best studied from a biochemical perspective are the archaeon, Pyrococcus furiosus, and the bacterium, Thermotoga maritima, both of which are saccharolytic. P. furiosus is thought to contain a new type of Entner-Doudoroff pathway for the conversion of carbohydrates ultimately to acetate, H2 and CO2. The pathway is independent of nicotinamide nucleotides and involves novel types of ferredoxin-linked oxidoreductases, one of which has tungsten, a rarely used element, as a prosthetic group. The only site of energy conservation is at the level of acetyl CoA, which is the presence of ADP and phosphate is converted to acetate and ATP in a single step. In contrast, T. maritima utilizes a conventional Embden-Meyerhof pathway for sugar oxidation. P. furiosus also utilizes peptides as a sole carbon and energy source. Amino acid oxidation is thought to involve glutamate dehydrogenase together with at least three types of novel ferredoxin-linked oxidoreductases which catalyze the oxidation of 2-ketoglutarate, aryl pyruvates and formaldehyde. One of these enzymes also utilizes tungsten. In P. furiosus, virtually all of the reductant that is generated during the catabolism of both carbohydrates and peptides is channeled to a cytoplasmic hydrogenase. This enzyme is now termed sulhydrogenase, as it reduces both protons to H2 and S degrees (or polysulfide) to H2S. S degrees reduction appears to lead to the conservation of energy in P. furiosus but not in T. maritima, although the mechanism by which this occurs is not known.

show abstract

Modeling the structure of pyrococcus furiosus rubredoxin by homology to other X‐ray structures

Cited by 15 publications

References 38 publications

Evidence for a Ternary Complex Formed between Flavodoxin and Cytochrome c3: 1H-NMR and Molecular Modeling Studies

Evidence for a Ternary Complex Formed between Flavodoxin and Cytochrome c3: 1H-NMR and Molecular Modeling Studies

Biochemical diversity among sulfur-dependent, hyperthermophilic microorganisms

Biochemical diversity among sulfur-dependent, hyperthermophilic microorganisms

Contact Info

Product

Resources

About