Rubredoxin: a new electron transfer protein from Clostridium pasteurianum.

Lovenberg, Walter; Sobel, Burton E.

doi:10.1073/pnas.54.1.193

Cited by 221 publications

(98 citation statements)

References 12 publications

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“…As expected from the growth conditions for P. furiosus, the rubredoxin from this organism (RdPf) exhibits significant thermostability, as the UV-visible and EPR properties of the protein are unaffected after a 24-h incubation at 95 "C (Blake et al, 1991). In contrast, rubredoxins from mesophilic bacteria are less thermostable; RdCp is rapidly denatured at 80 "C (Lovenberg & Sobel, 1965), whereas RdDg loses 50% of its visible absorption after -2 h at 80°C (Papavassilou & Hatchikian, 1985). Consequently, RdPf provides the opportunity to study factors that influence the extreme thermostability of this protein and hence to examine structural features that may be important to the thermostability of proteins in general.…”

Section: Figmentioning

confidence: 79%

“…In this discussion, the assumption is made that RdPf is more stable than the other rubredoxins of known structure. As mentioned in the introduction, it appears that RdPf is more stable than RdCp (Lovenberg & Sobel, 1965) and RdDg (Papavassilou & Hatchikian, 1985). No studies of the stabilities of either RdDd and RdDv have apparently been reported.…”

Section: Comparison To Other Rubredoxins Of Known Structurementioning

confidence: 98%

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X‐ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium pyrococcus furiosus

et al. 1992

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The structures of the oxidized and reduced forms of the rubredoxin from the archaebacterium, Pyrococcus furiosus, an organism that grows optimally at 100 °C, have been determined by X‐ray crystallography to a resolution of 1.8 å. Crystals of this rubredoxin grow in space group P212121 with room temperature cell dimensions a = 34.6 å, b = 35.5 å, and c = 44.4 å. Initial phases were determined by the method of molecular replacement using the oxidized form of the rubredoxin from the mesophilic eubacterium, Clostridium pasteurianum, as a starting model. The oxidized and reduced models of P. furiosus rubredoxin each contain 414 nonhydrogen protein atoms comprising 53 residues. The model of the oxidized form contains 61 solvent H2O oxygen atoms and has been refined with X‐PLOR and TNT to a final R = 0.178 with root mean square (rms) deviations from ideality in bond distances and bond angles of 0.014 å and 2.06°, respectively. The model of the reduced form contains 37 solvent H2O oxygen atoms and has been refined to R = 0.193 with rms deviations from ideality in bond lengths of 0.012 å and in bond angles of 1.95°. The overall structure of P. furiosus rubredoxin is similar to the structures of mesophilic rubredoxins, with the exception of a more extensive hydrogen‐bonding network in the β‐sheet region and multiple electrostatic interactions (salt bridge, hydrogen bonds) of the Glu 14 side chain with groups on three other residues (the amino‐terminal nitrogen of Ala 1; the indole nitrogen of Trp 3; and the amide nitrogen group of Phe 29). The influence of these and other features upon the thermostability of the P. furiosus protein is discussed.

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Section: Figmentioning

confidence: 79%

Section: Comparison To Other Rubredoxins Of Known Structurementioning

confidence: 98%

X‐ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium pyrococcus furiosus

et al. 1992

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“…They are found primarily in anaerobic bacteria, and are believed to be involved in electron transfer reactions. The redox potential for various rubredoxins range from -57 to 6 mV (Lovenberg & Sobel, 1965: Moura et al, 1979: LeGall et al, 1988: Adams, 1992 rubredoxins is not well understood, and it has been suggested that tuning of the redox potential is modulated by the protein environment. The protein matrix can alter the redox potential through the ligand field produced by the chelating residues and the electrostatic potential surrounding the metal center.…”

Section: Effect Of Metal-binding On Protein Structure and Stabilitymentioning

confidence: 99%

The de novo design of a rubredoxin‐like fe site

Farinas

Regan

1998

Protein Science

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A redox center similar to that of rubredoxin was designed into the 56 amino acid immunoglobulin binding B 1 domain of Streptococcals protein G. The redox center in rubredoxin contains an iron ion tetrahedrally coordinated by four cysteine residues, [ F e ( S -c~s )~] ",-'. The design criteria for the target site included taking backbone movements into account, tetrahedral metal-binding, and maintaining the structure and stability of the wild-type protein. The optical absorption spectrum of the Co(I1) complex of the metal-binding variant is characteristic of tetrahedral chelation by four cysteine residues. Circular dichroism and nuclear magnetic resonance measurements reveal that the metal-free and Cd(I1)-bound forms of the variant are folded correctly and are stable. The Fe(II1) complex of the metal-binding mutant reproduces the optical and the electron paramagnetic resonance spectra of oxidized rubredoxin. This demonstrates that the engineered protein chelates Fe(II1) in a tetrahedral array, and the resulting center is similar to that of oxidized rubredoxin.Keywords: de novo design; metalloprotein; protein engineering; rubredoxin Protein engineering and de novo design approaches have begun to afford a more detailed understanding of the balance of the forces that determine protein structure and function (Regan & DeGrado, 1988;Regan, 1993;Bryson et al., 1995;Regan, 1995;Dalal et al., 1997;Smith & Regan, 1997;Hellinga, 1998). To date, there are just a few examples of designed proteins that adopt a specified fold, and number which display novel activities is still smaller (Dill, 1990; Schafmeister et al., 1993;Jackson et al., 1994;Quinn et al., 1994;Yan & Erickson, 1994;Baltzer et al., 1996;Dahiyat & Mayo, 1997;Hill & DeGrado, 1998;QuCnCneur et al., 1998). A particular focus of functional design efforts has been the engineering of novel metal-binding sites. Metal-binding sites represent an attractive target because they play a variety of functions from stabilization of protein structure to catalytic roles such as the activation of water for nucleophilic attack, electron transfer, and redox activity. More recently, several groups have focused strongly on the design of metal-binding sites with particular activities in mind. For example, two metal-binding histidine residues have been engineered into rat trypsin to "switch" the catalytic activity on or off by disrupting the catalytic triad. The protein can be turned off by Cu(I1) chelation in the designed site and reactivated upon removal of Cu(I1) with EDTA (Halfon & Craik, 1996). In another design, a metal-binding site, based on the metal center of carbonic

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“…The purified enzyme is oxidized as indicated by a pink color and a UV spectrum consistent with an oxidized rubredoxin Fe-S center (18). The enzyme was reconstituted with Fe II in the presence of dithiothreitol; upon removal of reconstituting agents, the protein solution was colorless, consistent with a reduced rubredoxin Fe-S center.…”

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confidence: 98%

Tryptophan Catabolism: Identification and Characterization of a New Degradative Pathway

Colabroy

Begley

2005

J Bacteriol

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A new tryptophan catabolic pathway is characterized from Burkholderia cepacia J2315. In this pathway, tryptophan is converted to 2-amino-3-carboxymuconate semialdehyde, which is enzymatically degraded to pyruvate and acetate via the intermediates 2-aminomuconate and 4-oxalocrotonate. This pathway differs from the proposed mammalian pathway which converts 2-aminomuconate to 2-ketoadipate and, ultimately, glutarylcoenzyme A.Tryptophan has a variety of metabolic functions within the cell. It is incorporated into the polypeptide chains of enzymes and proteins, and it is the biosynthetic precursor of the cofactor NAD (19), the antibiotics anthramycin (15) and actinomycin (16), the siderophore quinolobactin (22), and the neurotransmitters serotonin (2) and melatonin (10,29). Tryptophan can also be fully catabolized. For example, Bacillus megaterium (1) and Rhodococcus erythropolis (27) can grow with tryptophan as their sole source of carbon and nitrogen, and several pseudomonads are capable of catabolizing tryptophan (26). Eukaryotes are also capable of breaking down excess tryptophan to CO 2 , NH 3 , and H 2 O. Labeling studies indicate that tryptophan degradation in mammals takes place via the kynurenine pathway, which is also used for NAD biosynthesis in all eukaryotic organisms and in a few bacterial species (9, 21, 24) (Fig. 1). On the kynurenine pathway, the branching point between NAD biosynthesis and complete tryptophan catabolism takes place at the intermediate 2-amino-3-carboxymuconate semialdehyde (ACMS) (Fig. 1). ACMS can cyclize nonenzymatically to yield quinolinate (5), the direct precursor to the pyridine ring of NAD, or it can be enzymatically decarboxylated by ACMS decarboxylase (ACMSD) (6, 7, 28). Although the biosynthesis of NAD via the kynurenine pathway is well understood, relatively little is known about the enzymology of tryptophan catabolism after ACMS. The recent discovery of the five enzymes necessary to biosynthesize ACMS from tryptophan in several prokaryotes (17) suggests that a complete tryptophan catabolic pathway, similar to the proposed human pathway, might also exist in bacteria.To test this hypothesis, we searched for clusters of tryptophan catabolic genes in bacteria by using 3-hydroxyanthranilate-3,4-dioxygenase (HAD) (11,20,23) and ACMSD (14,23,28) sequences from the NCBI database (http://www.ncbi.nlm .nih.gov) and by using the SEED database (http://theseed .uchicago.edu/FIG/index.cgi) for comparative genome analysis. Several bacteria that contained likely gene candidates for further degradation of ACMS clustered with HAD and ACMSD were identified. In Burkholderia cepacia J2315, HAD and ACMSD orthologs occurred in a cluster with genes of unknown function. Sequence analysis suggested that one of the unknown genes might function as a 2-aminomuconate semialdehyde dehydrogenase (AMDH; EC 1.2.1.32) (12) and another as a 2-aminomuconate deaminase (AMD; EC 3.5.99.5) (13,14).A second related genomic cluster was identified immediately upstream of the HAD-AMD cluster (Fig. 2). Within the se...

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Rubredoxin: a new electron transfer protein from Clostridium pasteurianum.

Cited by 221 publications

References 12 publications

X‐ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium pyrococcus furiosus

X‐ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium pyrococcus furiosus

The de novo design of a rubredoxin‐like fe site

Tryptophan Catabolism: Identification and Characterization of a New Degradative Pathway

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