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  • 1
    Electronic Resource
    Electronic Resource
    Molecular Evolution of the Myeloperoxidase Family (2000)
    Springer
    Journal of molecular evolution 51 (2000), S. 433-445 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Cyclooxygenase — Mosaic proteins — Heme
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Animal myeloperoxidase and its relatives constitute a diverse protein family, which includes myeloperoxidase, eosinophil peroxidase, thyroid peroxidase, salivary peroxidase, lactoperoxidase, ovoperoxidase, peroxidasin, peroxinectin, cyclooxygenase, and others. The members of this protein family share a catalytic domain of about 500 amino acid residues in length, although some members have distinctive mosaic structures. To investigate the evolution of the protein family, we performed a comparative analysis of its members, using the amino acid sequences and the coordinate data available today. The results obtained in this study are as follows: (1) 60 amino acid sequences belonging to this family were collected by database searching. We found a new member of the myeloperoxidase family derived from a bacterium. This is the first report of a bacterial member of this family. (2) An unrooted phylogenetic tree of the family was constructed according to the alignment. Considering the branching pattern in the obtained phylogenetic tree, together with the mosaic features in the primary structures, 60 members of the myeloperoxidase family were classified into 16 subfamilies. (3) We found two molecular features that distinguish cyclooxygenase from the other members of the protein family. (4) Several structurally deviated segments were identified by a structural comparison between cyclooxygenase and myeloperoxidase. Some of the segments seemed to be associated with the functional and/or structural differences between the enzymes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002390010106
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  • 2
    Electronic Resource
    Electronic Resource
    Molecular Evolution of the Photolyase–Blue-Light Photoreceptor Family (1997)
    Springer
    Journal of molecular evolution 45 (1997), S. 535-548 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Evolution — Protein — DNA photolyase — Blue-light photoreceptor — Phylogenetic analysis — Photoreactivation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The photolyase–blue-light photoreceptor family is composed of cyclobutane pyrimidine dimer (CPD) photolyases, (6-4) photolyases, and blue-light photoreceptors. CPD photolyase and (6-4) photolyase are involved in photoreactivation for CPD and (6-4) photoproducts, respectively. CPD photolyase is classified into two subclasses, class I and II, based on amino acid sequence similarity. Blue-light photoreceptors are essential light detectors for the early development of plants. The amino acid sequence of the receptor is similar to those of the photolyases, although the receptor does not show the activity of photoreactivation. To investigate the functional divergence of the family, the amino acid sequences of the proteins were aligned. The alignment suggested that the recognition mechanisms of the cofactors and the substrate of class I CPD photolyases (class I photolyases) are different from those of class II CPD photolyases (class II photolyases). We reconstructed the phylogenetic trees based on the alignment by the NJ method and the ML method. The phylogenetic analysis suggested that the ancestral gene of the family had encoded CPD photolyase and that the gene duplication of the ancestral proteins had occurred at least eight times before the divergence between eubacteria and eukaryotes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006258
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  • 3
    Electronic Resource
    Electronic Resource
    Molecular Evolution of the Domain Structures of Protein Disulfide Isomerases (1998)
    Springer
    Journal of molecular evolution 47 (1998), S. 200-210 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Evolution — Protein — Protein disulfide isomerase — Thioredoxin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Protein disulfide isomerase (PDI) is an enzyme that promotes protein folding by catalyzing disulfide bridge isomerization. PDI and its relatives form a diverse protein family whose members are characterized by thioredoxin-like (TX) domains in the primary structures. The family was classified into four classes by the number and the relative positions of the TX domains. To investigate the evolution of the domain structures, we aligned the amino acid sequences of the TX domains, and the molecular phylogeny was examined by the NJ and ML methods. We found that all of the current members of the PDI family have evolved from an ancestral enzyme, which has two TX domains in the primary structure. The diverse domain structures of the members have been generated through domain duplications and deletions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006377
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  • 4
    Electronic Resource
    Electronic Resource
    Identification of New Members of the GS ADP-Forming Family from the De Novo Purine Biosynthesis Pathway (1999)
    Springer
    Journal of molecular evolution 48 (1999), S. 482-492 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Protein — De novo purine biosynthesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Most living organisms can synthesize isosinate from 5-phosphoribosyl 1-pyrophosphate in the de novo purine biosynthesis pathway, which is basically composed of 10 reaction steps. Phosphoribosylglycinamide synthetase (GARS) catalyzes the second step of the pathway. We found that the enzyme shows weak, but significant, sequence similarity to phosphoribosylglycinamide formyltransferase 2 (GART2) and the ATPase domain of phosphoribosylaminoimidazole carboxylase (AIRCA), which catalyze the third and sixth steps of the pathway, respectively. In addition, the three enzymes were similar in amino acid sequence to biotin carboxylase (BC) and carbamoylphosphate synthetase (CPS), which are the members of the GS ADP-forming family. This family has been identified through a tertiary structure comparison and includes glutathione synthetase, d-alanine:d-alanine ligase, BC, succinyl-CoA synthetase β-chain, and phosphoribosylaminoimidazole-succinocarboxamide synthase. Molecular phylogenetic analysis based on a multiple alignment of GARS, GART2, AIRCA, BC, and CPS suggests that GART2 is more closely related to AIRCA than to GARS among the three enzymes from the pathway, though the three enzymes are relatively close to each other within the GS ADP-forming family. Moreover, the analysis showed that archaeal GARS had diverged before the speciation between bacteria and eucarya.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006492
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  • 5
    Electronic Resource
    Electronic Resource
    Membrane-bound Bacillus cytochromes c and their phylogenetic position among bacterial class I cytochromes c (1994)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 122 (1994), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract Gram-positive bacteria lack a periplasmic compartment and contain only membrane-bound cytochromes c. There are at least two types. One is found in subunit II of cytochrome oxidase, and the other is small cytochrome c which is also membrane-bound because of an unprocessed signal sequence or post-translational acylation at the N-terminal end of the protein. These Bacillus cytochromes c are compared with known class I cytochromes c, and a phylogenetic tree has been constructed by the neighbour-joining method.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1994.tb07168.x
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  • 6
    Electronic Resource
    Electronic Resource
    Mutational analysis of the functional motifs of RuvB, an AAA+ class helicase and motor protein for Holliday junction branch migration (2000)
    Oxford, UK : Blackwell Science Ltd
    Molecular microbiology 36 (2000), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: Escherichia coli RuvB protein, together with RuvA, promotes branch migration of Holliday junctions during homologous recombination and recombination repair. The RuvB molecular motor is an intrinsic ATP-dependent DNA helicase with a hexameric ring structure and its architecture has been suggested to be related to those of the members of the AAA+ protein class. In this study, we isolated a large number of plasmids carrying ruvB mutant genes and identified amino acid residues important for the RuvB functions by examining the in vivo DNA repair activities of the mutant proteins. Based on these mutational studies and amino acid conservation among various RuvBs, we identified 10 RuvB motifs that agreed well with the features of the AAA+ protein class and that distinguished the primary structure of RuvB from that of typical DNA/RNA helicases with seven conserved helicase motifs.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.2000.01842.x
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  • 7
    Electronic Resource
    Electronic Resource
    Cloning by functional expression of platelet-activating factor receptor from guinea-pig lung (1991)
    [s.l.] : Nature Publishing Group
    Nature 349 (1991), S. 342-346 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] FIG. 1 PAF-induced inward Cl~ current in Xenopus oocytes. a, The electrophy-siological response to PAF in an oocyte injected with the transcript made of a 6xl04-phage DNA library, b, The electrophysiological response to lyso-PAF and PAF in an oocyte injected with the transcript of the cloned PAF ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/349342a0
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  • 8
    Electronic Resource
    Electronic Resource
    Retroviral protease-like sequence in the yeast transposon Ty 1 (1985)
    [s.l.] : Nature Publishing Group
    Nature 315 (1985), S. 691-691 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] RECENTLY, Mellor et al.1 determined the nucleotide sequence of the 5'-terminal portion of the yeast transposon Tyl and identified two open reading frames, ORF1 and ORF2, which are in the same relative positions as the gag and pol coding sequences in retroviruses. In addition, they showed that Tyl ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/315691a0
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  • 9
    Electronic Resource
    Electronic Resource
    Sequence similarity between EGF receptor and α 1 -acid glycoprotein (1985)
    [s.l.] : Nature Publishing Group
    Nature 314 (1985), S. 199-199 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] THE human epidermal growth factor (EGF) receptor precursor consists of three domains, an extracellular EGF binding domain, a single transmembrane domain and a cytoplasmic domain. Ullrich et a/.1 recently determined the complete amino acid sequence of the molecule and showed that the latter two ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/314199a0
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  • 10
    Electronic Resource
    Electronic Resource
    Sequence homology between retroviral reverse transcriptase and putative polymerases of hepatitis B virus and cauliflower mosaic virus (1983)
    [s.l.] : Nature Publishing Group
    Nature 305 (1983), S. 827-829 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Homologies between distantly related proteins can be detected using the presently available data on the substitution frequencies between different pairs of amino acids10"12 (when proteins evolve under the constraints of maintaining their original functions, conservative amino acid substitutions are ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/305827a0
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