RESUMO
Cytochromes c are proteins that can be defined both phenotypically and by their possession of a characteristic sequence motif. Many sequences from bacterial sources are known, and new ones are being reported every year. An analysis can be made as to what fraction of new sequences are members of already known classes or subclasses, and how many map into previously uninhabited regions of sequence space.
Assuntos
Grupo dos Citocromos c/classificação , Sequência de Aminoácidos , Animais , Desulfovibrio/enzimologia , Methylococcaceae/enzimologia , Dados de Sequência Molecular , Conformação Proteica , Pseudomonas/enzimologia , Rodopseudomonas/enzimologia , Rhodospirillum rubrum/enzimologia , Homologia de Sequência do Ácido NucleicoRESUMO
Amino acid sequence studies show that the aliphatic amidase (EC 3.5.1.4) from Pseudomonas aeruginosa PAC142 consists of a single polypeptide chain of 346 residues, giving an Mr of 38,400. The evidence from the amino acid studies is in complete agreement with that deduced from the DNA sequence of the amiE gene. Studies of the protein from Pseudomonas putida A87 show that it differs from the Ps. aeruginosa protein by about 30 amino acid substitutions. It now becomes possible to relate changes in the enzyme which result in altered specificity to structural changes in the protein.
Assuntos
Amidoidrolases/análise , Pseudomonas aeruginosa/enzimologia , Sequência de Aminoácidos , Fragmentos de Peptídeos/análiseRESUMO
The amino acid sequence of the zinc-requiring beta-lactamase II from Bacillus cereus strain 569 has been determined. It consists of a single polypeptide chain of 227 residues. It is the only example so far fully characterized of a class B beta-lactamase, and is structurally and mechanistically distinct from both the widely distributed class A beta-lactamases (such as the Escherichia coli RTEM enzyme) and from the chromosomally encoded class C enzymes from Gram-negative bacteria.
Assuntos
Bacillus cereus/enzimologia , Cefalosporinase/análise , Zinco/metabolismo , beta-Lactamases/análise , Sequência de Aminoácidos , Brometo de Cianogênio/farmacologia , Fragmentos de Peptídeos/análiseRESUMO
Rhodospirillum salexigens is a moderately halophilic purple phototrophic bacterium which grows optimally in 8% NaCl. The amino acid sequences of the two principal soluble cytochromes c have been determined. One of these is a cytochrome c2, similar in size to mitochondrial cytochrome c. While clearly of the same sequence class as mitochondrial cytochrome c and the proteins from several other Gram-negative bacteria, it does not show particular affinity to any already known sequence in terms of the percentage sequence identity. The other protein is a cytochrome c', but is also a divergent member of this widespread group. The lack of appreciable sequence identity to other species is probably due to a limit of divergence which has been reached for the majority of purple bacterial species. However, the numbers of insertions and deletions and their locations in cytochromes c2 and c' suggest that R salexigens may be related to Rhodospirillum molischianum. Like other electron transport proteins from halophiles, both of these cytochromes are notable for their high content of arginine as compared with lysine and both are acidic. However, they do not show any particular sequence homology to electron transport proteins that have been characterized from the extremely halophilic phototrophes of the genus Ectothiorhodospira. Thus, it appears that adaptation to halophilic habitats has independently occurred more than once in purple bacteria.
Assuntos
Grupo dos Citocromos c/química , Rhodospirillum/metabolismo , Sequência de Aminoácidos , Animais , Citocromos c2 , Endopeptidases , Mitocôndrias/metabolismo , Dados de Sequência Molecular , Fragmentos de Peptídeos/química , Deleção de Sequência , Homologia de Sequência de AminoácidosRESUMO
A restriction enzyme map was constructed for 5.1-kb fragment of Pseudomonas aeruginosa DNA inserted into plasmid pBR322. Restriction enzyme sites were matched to the N-terminal amino acid sequence of amidase to obtain alignment of the amiE gene within the cloned fragment.
Assuntos
Amidoidrolases/genética , DNA Recombinante , Genes , Pseudomonas aeruginosa/genética , Sequência de Aminoácidos , Bacteriófago lambda , Clonagem Molecular , Enzimas de Restrição do DNA , Vetores Genéticos , PlasmídeosRESUMO
The beta-lactamases are widely distributed in both Gram-positive and Gram-negative bacteria. They all inactivate penicillins and cephalosporins by opening the beta-lactam ring. Many varieties of the enzyme can be distinguished on the basis of their catalytic and molecular properties, but only amino acid sequence determination gives information upon which a molecular phylogeny can be based. The present evidence suggests that the beta-lactamases have a polyphyletic origin. All the beta-lactamases of currently known amino acid sequence belong to one homology group, here called class A enzymes. Class B consists of the mechanistically distinct Bacillus cereus beta-lactamase II, which preliminary partial sequence analysis suggests to be structurally unrelated to the class A enzymes. It is predicted that sequence analysis will show that further classes will need to be created to account for particular beta-lactamases of distinctive molecular and mechanistic properties.
Assuntos
beta-Lactamases , Sequência de Aminoácidos , Bactérias/enzimologia , Evolução Biológica , Fenômenos Químicos , Química , Conformação ProteicaRESUMO
The amino acid sequence of the cytochrome c' from Alcaligenes sp. N.C.I.B. 11015 (Iwasaki's ;Pseudomonas denitrificans') has been determined. This organism is the only non-photosynthetic bacterium in which the protein has been found. The protein consists of a single polypeptide chain of 127 residues, with a single haem covalently attached to two cysteines. Unlike normal cytochromes c, the haem attachment site is very close to the C-terminus. The amino acid sequence around the haem attachment site is very similar to that of Chromatium vinosum D cytochrome c'. Detailed evidence for the amino acid sequence of the protein has been deposited as Supplementary Publication SUP 50022 at the British Library (Lending Division), (formerly the National Lending Library for Science and Technology), Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies may be obtained on the terms given in Biochem. J. (1973) 131, 5.
Assuntos
Grupo dos Citocromos c/análise , Pseudomonas/enzimologia , Alcaligenes/enzimologia , Sequência de Aminoácidos , Chromatium/enzimologia , Cromatografia em Gel , Cromatografia em Papel , Eletroforese em Papel , Heme , Microfilmagem , Papaína , PeptídeosRESUMO
Cytochrome c-551 was prepared from nine different strains of Pseudomonas aeruginosa and six of Pseudomonas fluorescens biotype C, and their amino acid sequences were compared with the sequences previously determined for the cytochromes of type strains of each species. The standard of sequence examination was such that all single amino acid substitutions, delections or insertions ought to have been detected. Balanced double changes in sites in the same part of the sequence might have escaped detection. The standard of some of the quantitative amino acid analyses was not as high as would be required for the investigation of completely unknown sequences. Eight of the Ps. aeruginosa sequences could not be distinguished from the type sequence, whereas the ninth had a single amino acid substitution. The sequences from Ps. fluorescens biotype C were more varied, differing in from zero to four substitutions from the type sequence, with the most diverse sequences differing in seven positions. The results for Ps. aeruginosa are interpreted as evidence that neutral mutations are not responsible for much molecular evolution. The superficially paradoxical differences in the results for the two species are discussed.
Assuntos
Evolução Biológica , Grupo dos Citocromos c/metabolismo , Pseudomonas aeruginosa/enzimologia , Pseudomonas fluorescens/enzimologia , Sequência de Aminoácidos , Aminoácidos/análise , Quimotripsina , Estabilidade de Medicamentos , Eletroforese em Gel de Amido , Variação Genética , Mutação , Fragmentos de Peptídeos/análise , Especificidade da EspécieRESUMO
Despite the revolution caused by information from macromolecular sequences, the basis of bacterial classification remains the genus and the species. How do these terms relate to the variety of bacteria that exist on earth? In this paper, the inter- and intraspecies differences in amino acid sequence of several bacterial electron transport proteins, cytochromes c, and blue copper proteins are compared. For the soil and water organisms studied, bacterial species can be classed as "tight" when there is little intraspecies variation, or "loose" when this variation is large. For this set of proteins and organisms, interspecies variation is much larger than that within a species. Examples of "tight" species are Pseudomonas aeruginosa and Rhodobacter sphaeroides, while Pseudomonas stutzeri and Rhodopseudomonas palustris are loose species. The results are discussed in the context of the origin and age of bacterial species, and the distribution of genomes in "sequence space." The situation is probably different for commensal or pathogenic bacteria, whose population structure and evolution are linked to the properties of another organism.
Assuntos
Bactérias/genética , Sequência de Aminoácidos , Animais , Bactérias/classificação , Evolução Molecular , Genes Bacterianos , Humanos , Dados de Sequência Molecular , Filogenia , Pseudomonas/genética , Rhodospirillaceae/genética , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Especificidade da EspécieRESUMO
The amino acid sequence of the penicillinase (penicillin amido-beta-lactamhydrolase, EC 3.5.2.6) from Staphylococcus aureus strain PC1 was determined. The protein consists of a single polypeptide chain of 257 residues, and the sequence was determined by characterization of tryptic, chymotryptic, peptic and CNBr peptides, with some additional evidence from thermolysin and S. aureus proteinase peptides. A mistake in the preliminary report of the sequence is corrected; residues 113-116 are now thought to be -Lys-Lys-Val-Lys- rather than -Lys-Val-Lys-Lys-. Detailed evidence for the amino acid sequence has been deposited as Supplementary Publication SUP 50056 (91 pages) at the British Library (Lending Division), Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies may be obtained on the terms given in Biochem. J. (1975) 145, 5.
Assuntos
Penicilinase/análise , Staphylococcus aureus/enzimologia , Amidas/análise , Sequência de Aminoácidos , Cromatografia em Gel , Cromatografia por Troca Iônica , Meios de Cultura , Brometo de Cianogênio , Eletroforese em Gel de Amido , Penicilinase/isolamento & purificação , Peptídeo Hidrolases , TetranitrometanoRESUMO
The amino acid sequences of two blue copper proteins from the pink facultative methylotroph Pseudomonas AM1 (N.C.I.B. 9133) were determined. They each consist of a single polypeptide chain and bind one copper atom. Amicyanin contains 99 and pseudoazurin 123 residues. Copper-binding sites, consisting of the side chains of two histidine, one cysteine and one methionine residues, can be recognized in each protein by analogy with azurin and plastocyanin, but the spacings of the ligand residues are different, and other sequence similarity is limited. Proteins that are in the pseudoazurin sequence class can be recognized in some strains of Alcaligenes, and probably also in Paracoccus denitrificans. Detailed evidence for the amino acid sequences of the proteins has been deposited as Supplementary Publication SUP 50130 (23 pp.) at the British Library (Lending Division), Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1985) 225, 5.
Assuntos
Azurina , Proteínas de Bactérias , Metaloproteínas , Pseudomonas/análise , Sequência de Aminoácidos , Azurina/análogos & derivadosRESUMO
The amino acid sequences of the cytochromes c-551 from three species of Pseudomonas have been determined. Each resembles the protein from Pseudomonas strain P6009 (now known to be Pseudomonas aeruginosa, not Pseudomonas fluorescens) in containing 82 amino acids in a single peptide chain, with a haem group covalently attached to cysteine residues 12 and 15. In all four sequences 43 residues are identical. Although by bacteriological criteria the organisms are closely related, the differences between pairs of sequences range from 22% to 39%. These values should be compared with the differences in the sequence of mitochondrial cytochrome c between mammals and amphibians (about 18%) or between mammals and insects (about 33%). Detailed evidence for the amino acid sequences of the proteins has been deposited as Supplementary Publication SUP 50015 at the National Lending Library for Science and Technology, Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1973), 131, 5.
Assuntos
Grupo dos Citocromos c/análise , Pseudomonas/análise , Acetona , Sequência de Aminoácidos , Aminoácidos/análise , Sulfato de Amônio , Proteínas de Bactérias/análise , Cromatografia em Gel , Cromatografia por Troca Iônica , Brometo de Cianogênio , Grupo dos Citocromos c/isolamento & purificação , Eletroforese em Gel de Amido , Estudos de Avaliação como Assunto , Formiatos , Heme , Concentração de Íons de Hidrogênio , Oxirredução , Peptídeos/análise , Pseudomonas/crescimento & desenvolvimento , Pseudomonas aeruginosa/análise , Pseudomonas fluorescens/análise , Especificidade da Espécie , Espectrofotometria , Termolisina , TripsinaRESUMO
The amino acid sequence of the plastocyanin from the green alga Chlorella fusca was determined. The protein consists of a single polypeptide chain of 98 residues, and was determined by characterization of chymotryptic and thermolysin peptides. The amino acid sequence shows considerable similarity to that of higher plant plastocyanins. The protein contains a single cysteine, and the sequence in the vicinity of this residue is similar to that around the cysteine residue of bacterial azurins. The plastocyanin contains some uncharacterized carbohydrate. Detailed evidence for the sequence of the protein has been deposited as Supplementary Publication SUP 50 036 (17pp., 1 microfiche) at the British Library (Lending Division) (formerly the National Lending Library for Science and Technology), Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies may be obtained on the terms given in Biochem. J. (1973) 131, 5.
Assuntos
Chlorella/análise , Proteínas de Plantas/análise , Plastocianina/análise , Sequência de Aminoácidos , Quimotripsina , Cisteína/análise , Fragmentos de Peptídeos/análise , TermolisinaRESUMO
Methylomonas J is an obligate methylotroph although it is unable to grow on methane. Like Pseudomonas AM1, it produces two blue copper proteins when growing on methylamine, one of which is the recipient of electrons from the methylamine dehydrogenase. When grown on methanol, only the other blue copper protein is produced. We have determined the amino acid sequences of these blue copper proteins, and show that they are both true azurins. The sequences are clearly homologous to those of the proteins characterized from fluorescent pseudomonads and various species of Alcaligenes, and can be aligned with them and with each other without the need to postulate any internal insertions or deletions in the sequences. The iso-1 azurin, the one produced during both methanol and methylamine growth, shows 59-65% identity with these other azurins, whereas the iso-2 protein shows only 47-53% identity. The proteins show 52% identity with each other. The two functionally equivalent blue copper proteins from Pseudomonas AM1 belong to two sequence classes that are quite distinct from the true azurins. Detailed evidence for the amino acid sequences of the proteins has been deposited as Supplementary Publication SUP 50151 (23 pages) at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1989) 257, 5.
Assuntos
Azurina , Proteínas de Bactérias , Methylococcaceae/metabolismo , Sequência de Aminoácidos , Transporte de Elétrons , Dados de Sequência MolecularRESUMO
The amino acid sequence of rattlesnake cytochrome c was originally reported in 1965, and was one of the earlier sequences to be studied. When compared with other mitochondrial cytochromes c, the snake sequence was soon seen to be anomalous. There were several positions in which the snake protein resembled human cytochrome c, although comparable anomalies were not reported for the protein from other reptiles such as lizard and turtle. Explanations of these results have included accelerated evolution in the snake lineage, paralogy rather than orthology, and faulty determination of the sequence, and the rattlesnake is now often omitted from cytochrome c phylogenetic trees. We have re-investigated the sequence of the snake protein, and believe that the correct sequence differs in nine places from that used for evolutionary theorizing since 1965. Four of these differences are near the haem-attachment site, in a region that was only analysed for amino acid composition in the original investigation. The other five differences are towards the C-terminus of the molecule, and can be explained as being due to the wrong ordering of amino acids within peptides that had been satisfactorily purified. Despite these corrections, the rattlesnake cytochrome c sequence still more closely resembles human cytochrome c than it does that of any other protein we know. We believe that this is an example of convergent evolution, although it does appear that there has been accelerated change in the line connecting the rattlesnake to the ancestral vertebrate line. Detailed evidence for the amino acid sequence of the protein has been deposited as Supplementary Publication SUP 50162 (16 pages) at the British Library Document Supply Centre, Boston Spa. Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1991) 273, 5.
Assuntos
Venenos de Crotalídeos/análise , Grupo dos Citocromos c/genética , Sequência de Aminoácidos , Animais , Evolução Biológica , Grupo dos Citocromos c/isolamento & purificação , Heme/metabolismo , Dados de Sequência Molecular , Homologia de Sequência do Ácido Nucleico , SerpentesRESUMO
Protein taxonomy has existed as a concept at least since 1958, but despite the efforts of the past 30 years, comparative studies of protein sequence, structure and distribution have not revolutionized any areas of systematics. The most interesting results of single gene phylogenies have been the anomalies, such as insulin in hystricomorphs or cytochrome c in the rattlesnake. It is likely that protein sequence information can be obtained in sufficient quality and quantity from ancient material as to change this finding? The paper will assess possibilities and the likely limitations of chemical studies of ancient protein material.