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At least 1,243 records · Page 69Linked to original sources
PubMed1982

Amino acid sequence of Synechocystis 6714 ferredoxin: a unique structural feature of unicellular blue-green algal ferredoxin.

The amino acid sequence of ferredoxin from Synechocystis 6714, a unicellular blue-green alga, was determined by a combination of conventional methods. The ferredoxin was composed of 96 amino acid residues and lacked methionine and tryptophan. The sequence was as follows: Ala-Ser-Tyr-Thr-Val-Lys-Leu-Ile-Thr- Pro-Asp-Gly-Glu-Asn-Ser-Ile-Glu-Cys-Ser-Asp-Asp-Thr-Tyr-Ile-Leu-Asp-Ala-Ala- Glu-Glu-Ala-Gly-Leu-Asp-Leu-Pro-Tyr-Ser-Cys-Arg-Ala-Gly-Ala-Cys-Ser-Thr-Cys- Ala-Gly-Lys-Ile-Thr-Ala-Gly-Ser-Val-Asp-Gln-Ser-Asp-Gln-Ser-Phe-Leu-Asp-Asp- Asp-Gln-Ile-Glu-Ala-Gly-Tyr-Val-Leu-Thr-Cys-Val-Ala-Tyr-Pro-Thr-Ser-Asp-Cys-Thr-Ile-Glu-Thr-His-Lys-Glu-Glu-Asp-Leu-Tyr. In an alignment of various ferredoxins with high homology from unicellular and filamentous blue-green algae, Synechocystis 6714 ferredoxin showed 4 gaps. Those between residues 9 and 10 and between residues 12 and 13 were unique for the ferredoxins from the unicellular algae Synechocystis 6714 and Aphanothece sacrum (ferredoxin I). Therefore, ferredoxins from unicellular algae were distinguishable from those of filamentous algae in terms of the presence of gaps. This feature appears to coincide with the phylogenetic division between the two types of blue-green algae.

Amino Acid Sequence↗
PubMed1999

The retrotransposon Osvaldo from Drosophila buzzatii displays all structural features of a functional retrovirus.

The Osvaldo retrotransposon has shown a high transposition rate in some strains of Drosophila buzzatii and in hybrids between D. buzzatii and its sibling D. koepferae. In order to understand the molecular basis of this phenomenon, we developed a procedure to clone a recently transposed copy with the aim of characterizing an active, full- length Osvaldo element. The complete nucleotide sequence of Osvaldo, obtained from a recent insertion site, was determined. Osvaldo is 9,045 bp long and is composed of a central coding region flanked by identical long terminal repeats (LTRs) of 1,196 bp each. Sequences homologous to the polypurine tract and tRNA-primer-binding site of retroviruses are located adjacent to the 3' and 5' LTRs, respectively. The internal region of Osvaldo contains three long open reading frames (ORFs 1, 2, and 3), comparable in size and location to gag, pol, and env retroviral genes. The conceptual translation of Osvaldo ORF1 exhibits sequence homology to HIV1 and SIV capsid (p24) and nucleocapsid (p7) mature proteins. ORF2 encodes the putative protease (PR), reverse transcriptase/ribonuclease H (RT/RH), integrase (IN), and a significant portion of the surface envelope (ENV) protein that is interrupted by a putative intron. A third ORF encodes the remaining part of the ENV protein. The predicted 62-kDa ENV protein shares several general features with membrane glycoproteins, including a potential signal peptide, a transmembrane domain near the C-terminus that could function as a membrane anchor, four consensus N-linked glycosylation motifs, and, finally, a potential protease cleavage site. The phylogenetic relationships of Osvaldo are explored, and they suggest that Osvaldo may constitute a new family of retroviruses in insects, distantly related to the previously described group of gypsy retroviruses.

Amino Acid Sequence↗
PubMed1999

Hmg-coA reductase gene family in cotton (Gossypium hirsutum L.): unique structural features and differential expression of hmg2 potentially associated with synthesis of specific isoprenoids in developing embryos.

As a first step towards understanding the biosynthesis of isoprenoids that accumulate in specialized pigment glands of cotton at the molecular level, two full-length genes (hmg1 and hmg2) were characterized encoding hmg-coA reductase (HMGR; EC 1.1.1.34), the enzyme that catalyzes the formation of a key isoprenoid precursor. Cotton hmgr genes exhibited features typical of other plant genes, however, hmg2 encodes the largest of all plant HMGR enzymes described to date. HMG2 contains several novel features that may represent functional specialization of this particular HMGR isoform. Such features include a unique 42 amino acid sequence located in the region separating the N-terminal domain and C-terminal catalytic domain, as well as an N-terminal hydrophobic domain that is not found in HMG1 or other HMGR enzymes. DNA blot analysis revealed that hmg1 and hmg2 belong to small subfamilies that probably include homeologous loci in allotetraploid cotton (Gossypium hirsutum L.). Ribonuclease protection assays revealed that hmg1 and hmg2 are differentially expressed in a developmentally- and spatially-modulated manner during morphogenesis of specialized terpenoid-containing pigment glands in embryos. Induced expression of hmg2 coincided with a possible commitment to sesquiterpenoid biosynthesis in developing embryos, although other developmental processes also requiring HMGR cannot be excluded.

Base Sequence↗
PubMed2001

Pectin degrading glycoside hydrolases of family 28: sequence-structural features, specificities and evolution.

Family 28 belongs to the largest families of glycoside hydrolases. It covers several enzyme specificities of bacterial, fungal, plant and insect origins. This study deals with all available amino acid sequences of family 28 members. First, it focuses on the detailed analysis of 115 sequences of polygalacturonases yielding their evolutionary tree. The large data set allowed modification of some of the existing family 28 sequence characteristics and to draw the sequence features specific for bacterial and fungal exopolygalacturonases discriminating them from the endopolygalacturonases. The evolutionary tree reflects both the taxonomy and specificity so that bacterial, fungal and plant enzymes form their own clusters, the endo- and exo-mode of action being respected, too. The only insect (animal) representative is most related to fungal endopolygalacturonases. The present study brings further: (i) the analysis of available rhamnogalacturonase sequences; (ii) the elucidation of relatedness between the recently added member, the endo-xylogalacturonan hydrolase and the rest of the family; and (iii) revealing the sequence features characteristic of the individual enzyme specificities and the evolutionary relationships within the entire family 28. The disulfides common for the individual enzyme groups were also proposed. With regard to functionally important residues of polygalacturonases, xylogalacturonan hydrolase possesses all of them, while the rhamnogalacturonases, known to lack the histidine residue (His223; Aspergillus niger polygalacturonase II numbering), have a further tyrosine (Tyr291) replaced by a conserved tryptophan. Evolutionarily, the xylogalacturonan hydrolase is most related to fungal exopolygalacturonases and the rhamnogalacturonases form their own cluster on the adjacent branch.

Amino Acid Sequence↗
PubMed2006

High (nuclear) grade adnexal carcinoma with microcystic adnexal carcinoma-like structural features.

Microcystic adnexal carcinoma (MAC) is a slow growing, locally aggressive sweat gland tumor. It predominantly affects the face and tends to recur despite local excision. Microscopically, MAC is characterized by a stratified proliferation of microcysts, cords, and ducts of cells that show squamous or adnexal differentiation. Atypia and mitoses are almost completely absent and metastatic deposits are rare and mostly limited to the regional lymph nodes; rather than real metastases, they might be the result of local extension of the tumor through perineurial spaces. We report a case of adnexal carcinoma with architectural features of MAC that displayed also marked nuclear pleomorphism and hyperchromasia with squamous pearl formation and a widespread strong p53 immunoreaction. The lesion behaved as a high-grade neoplasm with rapid growth, carcinosarcomatous metaplastic transformation in a relapse, and what were clinically suspected to be metastases. The literature contains several other examples reported as metastatic high-grade MAC, one of them with widespread distant metastases. We therefore want to sound an alert about the possible existence of tumors displaying microscopic findings characteristic of the aggressive forms of sweat gland carcinoma (nuclear pleomorphism and hyperchromasia, vascular invasion, and necrosis) in addition to architectural features of MAC. Whether these tumors should be called high-grade MACs or belong to a separate category remains an open issue until more cases are reported and bridge cases are eventually documented.

Aged↗
PubMed1993

Analysis of pathotype-specific structural features and cleavage activation of Newcastle disease virus membrane glycoproteins using antipeptide antibodies.

Peptides were synthesized, that correspond to cleaved and trimmed carboxyl termini of the F2 polypeptide regions of fusion (F) protein precursors (F0 proteins) in four different strains of Newcastle disease virus (NDV). These peptides differed only within the four carboxyl-terminal residues and represent F2 polypeptides of virulent (AV), low-virulence (EG) and avirulent (V4 and WA) pathotypes of NDV. Polyclonal rabbit antisera against each peptide reacted with their corresponding monomeric F2 polypeptides and F protein oligomers as analysed by immunoblotting of egg-propagated virions. Bidirectional cross-reactivity was observed between V4 and EG antisera and F2 polypeptides which differ only by a single variation of lysine and arginine at position 3 from their carboxyl termini. The other two antisera (AV and WA) were specific for their corresponding F2 polypeptides. All of these antisera were shown to react in a strain-specific manner with intact egg-propagated virions in an ELISA. A previously described antiserum, designed to target the haemagglutinin-neuraminidase (HN) protein precursor (HN0 protein) of avirulent strains of NDV, has been shown to be specific for residual HN0 protein of avirulent virions propagated in embryonated chicken eggs. Whereas the antiserum targeted at the carboxyl terminus of the V4 F2 polypeptide did not react with F0 proteins of cell culture-propagated strains in immunoblotting, antipeptide antibodies targeted at another region of the F2 polypeptide and a segment of the F1 polypeptide did react with the F0 protein from infected cells. These data are consistent with inclusion of the terminal carboxylate of the F2 polypeptides in the recognition determinants of the antibodies targeted at the carboxyl terminus of the V4 F2 polypeptide. The antisera described herein are ideally suited to rapid immunochemical pathotyping of NDV isolates and immunochemical characterization of the sites of intracellular cleavage activation of F0 and HN0 proteins and may be useful for defining interactions involved in F protein folding.

Amino Acid Sequence↗
PubMed2001

Creating structure features by data mining the PDB to use as molecular-replacement models.

Mathematical data-mining techniques to generate a representative set of protein fragments are described. Protein fragments are used as search models within the macromolecular phasing method of molecular replacement to attempt to phase protein data without a homologous model correctly. Preliminary investigations using these fragments indicate that molecular replacement with AMoRe is not sensitive enough to phase myoglobin or insulin data sufficiently for successful refinement. The results suggest that more advanced molecular replacement techniques may be successful, though at present these are not computationally practical.

Amino Acid Motifs↗
PubMed1991

Mutational analysis supports a role for multiple structural features in the C-terminal secretion signal of Escherichia coli haemolysin.

We have carried out an extensive mutational analysis of the C-terminal signal which targets the export of the 1024-residue haemolysin protein (HlyA) of Escherichia coli across both bacterial membranes into the surrounding medium. Over 60 variants of the HlyA C-terminal 53-amino-acid sequence were created by oligonucleotide-directed mutagenesis and fused to the HlyA N-terminal 830 residues. Transport of the HlyA derivatives by the HlyB/HlyD system was compared with the wild-type level and the data indicate that the HlyA C-terminal export signal lies within the last 48 amino acids and comprises three functional domains: an amphipathic, charged helix between residues 1,977 and R,996; a 13-amino-acid uncharged region from residue T,997 to S,1009; and an 8-amino-acid hydroxylated tail at the extreme C-terminus. Analogous features were found in the C-terminal sequences of an extended family of haemolysins, leukotoxins and proteases which are secreted by HlyB/HlyD-type translocators. In particular, all nine proteins which are secreted into the extracellular medium possess potential extended amphipathic helices. These results suggest a possible role for multiple regions of the HlyA C-terminal export signal in which the first two domains span the membranes and the third domain remains in the cytoplasm.

Amino Acid Sequence↗