The amino acid sequence of ferredoxin from Clostridium acidi-urici

Comparison of proteins from thermophilic and nonthermophilic sources in terms of structural parameters inferred from amino acid composition

The amino acid composition of 14 different proteins from thermophilic bacteria were compiled along with the amino acid compositions of 56 corresponding proteins from nonthermophilic sources. A comparison was made between proteins serving the same catalytic function, and significant differences in composition were noted for those proteins from thermophilic bacteria. However, no consistent pattern was evident and the differences were often small. The two data pools were treated as two distinct classes and a thermophilic versus non-thermophilic comparison of amino acid composition was made using the Student's t-test. Significant differences in composition were found for Asx (sum of Asp and Asn, if known), Ser, and Arg. Both classes of data have similar standard deviations for the mean of any single amino acid, suggesting a similar tolerance of variation in the two classes of proteins. This would argue against the hypothesis that thermophiles exhibit a greater frequency of errors in protein synthesis. The amino acid compositions were used to calculate structural parameters (% helix, % beta, % turn, hydrophobicity, and melting temperatures) for the two classes of proteins. Of these, only the predicted % beta content was significantly lower for proteins of thermophilic origin. No differences in hydrophobicity or predicted melting temperature were observed for the two classes of proteins. This study supports the hypothesis that while small differences may occur in the amino acid composition of thermophilic proteins, they are quite varied and often are very subtle.

Refined crystal structure of the 2[4Fe-4S] ferredoxin from Clostridium acidurici at 1.84 A resolution

The crystal structure of the 2[4Fe-4S] ferredoxin from Clostridium acidurici has been determined at a resolution of 1.84 A and refined to an R-factor of 0.169. Crystals belong to space group P4(3)2(1)2 with unit cell dimensions a = b = 34.44 A and c = 74.78 A. The structure was determined by molecular replacement using the previously published model of an homologous ferredoxin and refined by molecular dynamics techniques. The model contains the protein and 46 water molecules. Only two amino acid residues, Asp27 and Asp28, are poorly defined in the electron density maps. The molecule has an overall chain fold similar to that of other [4Fe-4S] bacterial ferredoxins of known structure. The two [4Fe-4S] clusters display similar bond distances and angles. In both of them the co-ordination of one iron atom (bound to Cys11 and Cys40) is slightly distorted as compared with that of the other iron atoms. A core of hydrophobic residues and a few water molecules contribute to the stability of the structure. The [4Fe-4S] clusters interact with the polypeptide chain through eight hydrogen bonds each, in addition to the covalent Fe-Scys bonds. The ferredoxin from Clostridium acidurici is the most typical clostridial ferredoxin crystallized so far and the biological implications of the newly determined structure are discussed.

Calculation of the redox potentials of iron-sulfur proteins: the 2-/3-couple of [Fe4S*4Cys4] clusters in Peptococcus aerogenes ferredoxin, Azotobacter vinelandii ferredoxin I, and Chromatium vinosum high-potential iron protein

Calculations of the redox potentials of the 2-/3-couples of [Fe4S*4Cys4] clusters in the iron-sulfur proteins Peptococcus aerogenes ferredoxin (PaFd), Azotobacter vinelandii ferredoxin I (AvFdI) and Chromatium vinosum high potential iron protein (CvHiPIP) based on the Protein Dipoles Langevin Dipoles (PDLD) method are reported. The structures of these proteins have been determined by X-ray crystallography; in the case of PaFd the structure has recently been revised due to a change in the sequence close to Cluster II. The large differences between the potentials of the [Fe4S*4Cys4] clusters of PaFd and AvFdI and the potential of the [Fe4S*4Cys4] cluster of CvHiPIP are successfully modeled and originate principally in differences in the configuration of main-chain amide groups near the clusters. The small difference between the potentials of PaFd and AvFdI is also satisfactorily modeled in the case of Cluster I of PaFd. Solvent dipoles close to the cluster in PaFd are an important contributor to its higher potential. The two X-ray structures of PaFd yield similar results for Cluster I of PaFd. In contrast, the results for Cluster II differ substantially; for reasons not yet clear, the recently revised structure leads to results in worse agreement with experiment.

Primary structure of nuclease P1 from Penicillium citrinum

The primary structure of nuclease P1, which cleaves both RNA and single-stranded DNA, from Penicillium citrinum was elucidated. The complete amino acid sequence consisting of 270 residues was determined by analysis of peptides obtained by digestion with Achromobacter protease I of the reduced and S-aminoethylated protein and by digestion with Staphylococcus aureus V8 protease of the reduced and S-carboxymethylated protein. Four half-cystine residues were assigned to Cys72-Cys217 and Cys80-Cys85. N-Glycosylated asparagine residues were identified at positions 92, 138, 184 and 197. Fast-atom-bombardment and laser-ionization MS were successfully used to confirm the determined amino acid sequences of peptides and to estimate the molecular mass of this glycoprotein having heterogenous sugar moieties, respectively. Comparison of the amino acid sequence of nuclease P1 with other nucleases revealed that the protein has a high degree of sequence identity (50%) with nuclease S1 from Aspergillus oryzae. The His-Phe-Xaa-Asp-Ala sequence (positions 60-64) is similar to the sequence (His-Phe-Asp-Ala) involving the active-site His119 of bovine pancreatic RNase A, and the Pro-Leu-His sequence (positions 124-126) is identical with the sequence involving the active-site His134 of porcine pancreatic DNase I.

Amino-acid sequence of ribonuclease T2 from Aspergillus oryzae

The amino acid sequence of ribonuclease T2 (RNase T2) from Aspergillus oryzae has been determined. This has been achieved by analyzing peptides obtained by digestions with Achromobacter lyticus protease I, Staphylococcus aureus V8 protease, and alpha-chymotrypsin of two large cyanogen bromide peptides derived from the reduced and S-carboxymethylated or S-aminoethylated protein. Digestion with A. lyticus protease I was successfully used to degrade the N-terminal half of the S-aminoethylated protein at cysteine residues. RNase T2 is a glycoprotein consisting of 239 amino acid residues with a relative molecular mass of 29,155. The sugar content is 7.9% (by mass). Three glycosylation sites were determined at Asns 15, 76 and 239. Apparently RNase T2 has a very low degree of sequence similarity with RNase T1, but a considerable similarity is observed around the amino acid residues involved in substrate recognition and binding in RNase T1. These similar residues may be important for the catalytic activity of RNase T2.

New perspectives on bacterial ferredoxin evolution

Recent evidence indicates that a gene transposition event occurred during the evolution of the bacterial ferredoxins subsequent to the ancestral intrasequence gene duplication. In light of this new information, the relationships among the bacterial ferredoxins were reexamined and an evolutionary tree consistent with this new understanding was derived. The bacterial ferredoxins can be divided into several groups based on their sequence properties; these include the clostridial-type ferredoxins, the Azotobacter-type ferredoxins, and a group containing the ferredoxins from the anaerobic, green, and purple sulfur bacteria. Based on sequence comparison, it was concluded that the amino-terminal domain of the Azotobacter-type ferredoxins, which contains the novel 3Fe:3S cluster binding site, is homologous with the carboxyl-terminal domain of the ferredoxins from the anaerobic photosynthetic bacteria. A number of ferredoxin sequences do not fit into any of the groups described above. Based on sequence properties, these sequences can be separated into three groups: a group containing Methanosarcina barkeri ferredoxin and Desulfovibrio desulfuricans ferredoxin II, a group containing Desulfovibrio gigas ferredoxin and Clostridium thermoaceticum ferredoxin, and a group containing Desulfovibrio africanus ferredoxin I and Bacillus stearothermophilus ferredoxin. The last two groups differ from all of the other bacterial ferredoxins in that they bind only one Fe:S cluster per polypeptide, whereas the others bind two. Sequence examination indicates that the second binding site has been either partially or completely lost from these ferredoxins. Methanosarcina barkeri ferredoxin and Desulfovibrio desulfuricans ferredoxin II are of interest because, of all the ferredoxins whose sequences are presently known, they show the strongest evidence of internal gene duplication.(ABSTRACT TRUNCATED AT 400 WORDS)

Complete amino acid sequence of the 4Fe-4S, thermostable ferredoxin from Clostridium thermoaceticum

The complete amino acid sequence of the 4Fe-4S ferredoxin from the thermophilic bacterium Clostridium thermoaceticum has been determined. The protein is extremely thermostable and is the only known clostridial ferredoxin to contain a single [4Fe-4S] cluster. The sequence totals 63 residues and includes the first tryptophan (Trp-26) reported for a clostridial ferredoxin, and other amino acids not commonly found in clostridial or clostridial-like ferredoxins: methionine (Met-1), histidine (His-33), arginine (Arg-49), and leucine (Leu-9, -19, and -31). Sequence homology to clostridial and other 8Fe-8S ferredoxins is limited to eight to nine residues at the amino-terminal sulfhydryl grouping (Cys-10, -13, -16, and -20) and two to five residues in the carboxyterminal region. This ferredoxin is, thus, sequentially distinct from all known clostridial ferredoxins and from other bacterial ferredoxins in both the 8Fe-8S and 4Fe-4S classes.

Comparative studies of two ferredoxins from Desulfovibrio desulfuricans norway

Two ferredoxins isolated from Desulfovibrio desulfuricans Norway have been purified and characterized. The less acidic, designated as ferredoxin I, contains four iron atoms, four acid-labile sulfur groups and six cysteine residues per molecule. Ferredoxin II is more acidic and abundant than ferredoxin I, but is very unstable to O2. Ferredoxin I and ferredoxin II differ according to amino acid composition but are homologous with respect to their N-terminal amino acid sequence. The absorption spectra of the two ferredoxins are similar to those of other Desulfovibrio species. Both proteins appear to be dimers of identical 6000-dalton subunits. Their activity was tested in two types of reaction in the electron transfer chain (phosphoroclastic reaction and sulfite reductase activity). The isolation of two different ferredoxins from the same organism, Desulfovibrio, has been reported in Desulfovibrio africanus but the significance of two ferredoxins functioning in the same electron transfer chain is not yet understood.

Thermal stability and protein structure

Amino acid sequences have been compared for thermophilic and mesophilic molecules of ferredoxin, glyceraldehyde-3-phosphate dehydrogenase, and lactate dehydrogenase. It is shown that Gly, Ser, Ser, Lys, and Asp in mesophiles are generally substituted by Ala, Ala, Thr, Arg, and Glu, respectively, in thermophiles. These exchanges suggest that thermal stability can be achieved by the addition of many small changes throughout the molecule without significant change in the backbone conformation. Their overall effect is primarily to increase internal and decrease external hydrophobicity as well as to favor helix stabilizing residues in helices. These substitutions minimize interruption of function or internal residue packing arrangements. Although the analysis has been confined to the above-mentioned molecules, the observed stabilizing principles may be more generally applicable.

Ferredoxin and formyltetrahydrofolate synthetase: comparative studies with Clostridium acidiurici, Clostridium cylindrosporum, and newly isolated anaerobic uric acid-fermenting strains

Six strains of Clostridium acidiurici and three strains of C. cylindrosporum were isolated from soil samples by enrichment culture with uric acid as the source of carbon, nitrogen, and energy. The newly isolated strains were characterized by their spore morphology and the amounts of glycine and formate formed by the fermentation of uric acid. The strains were easily identified as belonging to one species or the other on the basis of spore morphology and formate production. The crystal properties and spectra of the native ferredoxins of all the strains isolated and the amino acid composition and partial carboxy-terminal sequence of all their apoferredoxins were determined. All the ferredoxins were tested for cross-reactivity with antiserum to C. acidiurici ferredoxin by microcomplement fixation. Five of the six C. acidiurici strains, which had ferredoxins with amino acid compositions identical to that from C. acidiurici, also showed immunological identity (immunological distance = 0.0). These results suggest sequence identity. The one strain with a different amino acid composition failed to show complete cross-reactivity. Two of the three C. cylindrosporum strains have ferredoxin amino acid compositions identical to that from C. cylindrosporum. The third strain had a minimum of five differences in sequence. All C. cylindrosporum strains had ferredoxins that differed considerably from C. acidiurici strains (minimum of eight to nine differences), and none of these ferredoxins cross-reacted with antisera to C. acidiurici ferredoxin. Antisera were prepared to formyltetrahydrofolate synthetase from C. acidiurici and C. cylindrosporum, and all possible comparisons were made by using immunodiffusion and microcomplement fixation. There is more intraspecies variation in the synthetases than in the ferredoxins; however, the results suggest considerable interspecies differences in both proteins. These results suggest a low degree of genomic relatedness between the two species, which contrasts sharply with their apparent high degree of phenotypic similarity.

Comparative immunochemistry of bacterial, algal and plant ferredoxins

1. Antibodies were produced in rabbits to the 4Fe-4S ferrodoxins from Bacillus stearothermophilus, the 2 [4Fe-4S] ferredoxin from Clostridium pasteurianum, and the 2Fe-2S ferredoxins from the blue-green algia Spirulina maxima, the green alga Scenedesmus obliquus, and the higher plant Beta vulgaris. The antibodies were tested for immunoprecipitation activity with seven bacterial, twelve blue-green algal, six eukaryotic algal and six higher plant ferredoxins. 2. Antibodies to the bacterial ferredoxins reacted to a significant extent only with their homologous proteins. On the other hand, antibodies to the plant and algal ferredoxins showed cross-reaction with other ferredoxins. There was a correlation between the degrees of immunoprecipitation and the similarity in amino acid sequences. These results suggest that the method can be used as a marker in taxonomic studies. 3. The interaction of the antibodies with the five native ferredoxins was compared with the reactions with their apoproteins. In each case the degree of interaction was different. This behaviour was interpreted as due to an influence of tertiary structure on the antibody-antigen interaction.

Letter: Sequences of the N-terminus portions of biliproteins

The N-terminal sequences of the separated polypeptide chains of biliproteins isolated from several Cyanophyta, Rhodophyta, and Cryptophyta have been determined. The portions of the sequences determined for the alpha (fast) chain of C-phycocyanin from both procaryotic and eucaryotic cells are extremely conservative. Methionine is the N-terminal amino acid in most of the species studied. The N-terminus and subsequent sequence of phycoerythrin alpha chains are almost identical with those of the C-phycocyanin alpha chain. The beta (slow) chain of C-phycocyanin is also rather conservative in amino acid substitution but has more variation than the alpha chain. The variations are consistent with single base changes in codons and conserve the size and functional characteristics of the amino acid. The sequence homologies are consistent with the phylogenetic relationship between Cyanophyta and the chloroplast of Rhodophyta. There are no other reported sequences of polypeptide chains of the same or related proteins from such different strains of microorganisms that show such close sequence homology.

Phylogenies from amino acid sequences aligned with gaps: the problem of gap weighting

The common but generally overlooked problem of how best to construct phylogenies from orthologous amino acid sequences, when their alignment requires the placement therein of gaps denoting insertions/deletions in the evolutionary history of their genes since their common ancestor, has been studied. Three diverse methods were examined: 1. each missing residue in a gap is weighted as equivalent to the average number of minimum nucleotide replacements in known conjugate amino acid pairs of those same two sequences, which weight necessarily differs for each pair of sequences; 2. each missing residue in a gap is weighted as equivalent to a fixed number of nucleotide replacements; and 3. each gap, regardless of length, is weighted as equivalent to a fixed number of nucleotide replacements. For the flavodoxins, each method yielded a different best tree and suggests that the choice of method may be crucial. For the plant ferredoxins, all methods give results inconsistent with botanical classification and suggests the sequences may not all be orthologous. For the bacterial ferredoxins, the method was less germane than the actual weight used, five different best trees being obtained depending upon the weight. The best tree for all ferredoxins (prokaryotic plus eukaryotic) combined proved to be greatly dependent upon the gap locations with several reasonable aligments yielding different best trees. They also suggest that functional equivalence may well prove to be a poor guide to which residues have a common ancestral codon. The rubredoxin sequences show that a partial internal gene duplication occurred in the Pseudomonas line, probably very soon after its divergence from the other genera. Together, the results clearly indicate that the phylogenetic answer one gets may greatly depend upon how one treats the gaps but they fail to indicate what treatment may be best.

Synthesis and properties of Clostridium acidi-urici (Leu2)-ferredoxin: a function of the peptide chain and evidence against the direct role of the aromatic residues in electron transfer

Tyrosyl or other aromatic residues generally occur in two conserved positions in the peptide chain of clostridial-type ferredoxins and have been implicated in the electron transfer function of these iron-sulfur proteins. We have prepared and determined some of the properties of a derivative of Clostridium acidi-urici ferredoxin, [Leu(2)]-ferredoxin, in which a leucyl residue has been substituted for the tyrosyl residue in position 2 from the amino terminus. [Leu(2)]-ferredoxin is fully active as an electron carrier in two biological assays, the phosphoroclastic enzyme system and the ferredoxin-dependent reduction of cytochrome c in the presence of ferredoxin-TPN reductase and TPNH. Quantitative electron paramagnetic resonance experiments indicate that [Leu(2)]-ferredoxin accepts nearly two electrons upon enzymatic reduction by pyruvate-ferredoxin oxidoreductase and an excess of pyruvate. If electron transfer to an iron-sulfur cluster is the rate-limiting step in the assays used, and if the rate of electron transfer through Tyr(30) is not much faster than through Tyr(2), these results indicate that the primary pathway of electron transfer in clostridial-type ferredoxins is not via Tyr or other aromatic amino-acid residues. The syntheses of other ferredoxin derivatives with amino-acid substitutions or deletions in positions 1 and 2 indicate that a large bulky residue, but not necessarily an aromatic residue, is needed in position 2 for the stability of this ferredoxin. The residue in position 2, therefore, appears to act as a hydrophobic shield for an iron-sulfur cluster.

The possible role of aromatic residues of Clostridium acidi-urici ferredoxin in electron transport

The (13)C-resonances of the 2',6'-ring carbon atoms of both tyrosyl residues of Clostridium acidi-urici ferredoxin are shifted downfield in the oxidized and reduced protein relative to these resonance positions in free tyrosine. These results show that both tyrosyl residues in the oxidized and reduced protein are in magnetically equivalent environments, and suggest that both tyrosyl residues are close to the two iron-sulfur clusters in the reduced and oxidized proteins and that each cluster is equally accessible to one reducing electron.

Amino acid composition and terminal sequences of ferredoxins from two photosynthetic green bacteria

The amino acid composition of ferredoxins from Chlorobium thiosulfatophilum 8327 and Chloropseudomonas ethylicum, like C. thiosulfatophilum Tassajara, resembled ferredoxins from nonphotosynthetic anaerobes rather than Chromatium; the terminal sequences, however, more closely resembled Chromatium ferredoxin.