Homologues of insulinase, a new superfamily of metalloendopeptidases

On the basis of a statistical analysis of an alignment of the amino acid sequences, a new superfamily of metalloendopeptidases is proposed, consisting of human insulinase, Escherichia coli protease III and mitochondrial processing endopeptidases from Saccharomyces and Neurospora. These enzymes do not contain the ‘HEXXH’ consensus sequence found in all previously recognized zinc metalloendopeptidases.

Download Full-text

Roles of the C-Terminal Amino Acids of Non-Hexameric Helicases: Insights from Escherichia coli UvrD

International Journal of Molecular Sciences ◽

10.3390/ijms22031018 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1018

Author(s):

Hiroaki Yokota

Keyword(s):

Escherichia Coli ◽

Amino Acids ◽

Amino Acid ◽

Single Molecule ◽

Underlying Mechanism ◽

Amino Acid Sequences ◽

E Coli ◽

X Ray Crystallography ◽

Terminal Amino

Helicases are nucleic acid-unwinding enzymes that are involved in the maintenance of genome integrity. Several parts of the amino acid sequences of helicases are very similar, and these quite well-conserved amino acid sequences are termed “helicase motifs”. Previous studies by X-ray crystallography and single-molecule measurements have suggested a common underlying mechanism for their function. These studies indicate the role of the helicase motifs in unwinding nucleic acids. In contrast, the sequence and length of the C-terminal amino acids of helicases are highly variable. In this paper, I review past and recent studies that proposed helicase mechanisms and studies that investigated the roles of the C-terminal amino acids on helicase and dimerization activities, primarily on the non-hexermeric Escherichia coli (E. coli) UvrD helicase. Then, I center on my recent study of single-molecule direct visualization of a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C) used in studies proposing the monomer helicase model. The study demonstrated that multiple UvrDΔ40C molecules jointly participated in DNA unwinding, presumably by forming an oligomer. Thus, the single-molecule observation addressed how the C-terminal amino acids affect the number of helicases bound to DNA, oligomerization, and unwinding activity, which can be applied to other helicases.

Download Full-text

Isolation and characterization of some novel genes of the apolipoprotein A-I family in Japanese eel, Anguilla japonica

Open Life Sciences ◽

10.2478/s11535-011-0042-8 ◽

2011 ◽

Vol 6 (4) ◽

pp. 545-557 ◽

Cited By ~ 2

Author(s):

Malay Choudhury ◽

Takahiro Oku ◽

Shoji Yamada ◽

Masaharu Komatsu ◽

Keita Kudoh ◽

...

Keyword(s):

Amino Acids ◽

Molecular Weight ◽

Amino Acid ◽

Consensus Sequence ◽

Structural Features ◽

Lipid Binding ◽

Japanese Eel ◽

Amino Acid Sequences ◽

Novel Genes ◽

Isolation And Characterization

AbstractApolipoproteins such as apolipoprotein (apo) A-I, apoA-IV, and apoE are lipid binding proteins synthesized mainly in the liver and the intestine and play an important role in the transfer of exogenous or endogenous lipids through the circulatory system. To investigate the mechanism of lipid transport in fish, we have isolated some novel genes of the apoA-I family, apoIA-I (apoA-I isoform) 1–11, from Japanese eel by PCR amplification. Some of the isolated genes of apoIA-I corresponded to 28kDa-1 cDNAs which had already been deposited into the database and encoded an apolipoprotein with molecular weight of 28 kDa in the LDL, whereas others seemed to be novel genes. The structural organization of all apoIA-Is consisted of four exons separated by three introns. ApoIA-I10 had a total length of 3232 bp, whereas other genes except for apoIA-I9 ranged from 1280 to 1441 bp. The sequences of apoIA-Is at the exon-intron junctions were mostly consistent with the consensus sequence (GT/AG) at exon-intron boundaries, whereas the sequences of 3′ splice acceptor in intron 1 of apoIA-I1-7 were (AC) but not (AG). The deduced amino acid sequences of all apoIA-Is contained a putative signal peptide and a propeptide of 17 and 5 amino acid residues, respectively. The mature proteins of apoIA-I1-3, 7, and 8 consisted of 237 amino acids, whereas those of apoIA-I4-6 consisted of 239 amino acids. The mature apoIA-I10 sequence showed 65% identity to amino acid sequence of apoIA-I11 which was associated with an apolipoprotein with molecular weight of 23 kDa in the VLDL. All these mature apoIA-I sequences satisfied the common structural features depicted for the exchangeable apolipoproteins such as apoA-I, apoA-IV, and apoE but apoIA-I11 lacked internal repeats 7, 8, and 9 when compared with other members of apoA-I family. Phylogenetic analysis showed that these novel apoIA-Is isolated from Japanese eel were much closer to apoA-I than apoA-IV and apoE, suggesting new members of the apoA-I family.

Download Full-text

Diarrhea-Inducing Activity of Avian Rotavirus NSP4 Glycoproteins, Which Differ Greatly from Mammalian Rotavirus NSP4 Glycoproteins in Deduced Amino Acid Sequence, in Suckling Mice

Journal of Virology ◽

10.1128/jvi.76.11.5829-5834.2002 ◽

2002 ◽

Vol 76 (11) ◽

pp. 5829-5834 ◽

Cited By ~ 44

Author(s):

Yoshio Mori ◽

Mohammed Ali Borgan ◽

Naoto Ito ◽

Makoto Sugiyama ◽

Nobuyuki Minamoto

Keyword(s):

Escherichia Coli ◽

Amino Acid ◽

Amino Acid Sequence ◽

Amino Acid Sequences ◽

Amino Acid Residues ◽

Suckling Mice

ABSTRACT Avian rotavirus NSP4 glycoproteins expressed in Escherichia coli acted as enterotoxins in suckling mice, as did mammalian rotavirus NSP4 glycoproteins, despite great differences in the amino acid sequences. The enterotoxin domain of PO-13 NSP4 exists in amino acid residues 109 to 135, a region similar to that reported in SA11 NSP4.

Download Full-text

Antigenic Relatedness and Partial Amino Acid Sequences of Pili of Escherichia coli Serotypes O1, O2, and O78 Pathogenic to Poultry

Avian Diseases ◽

10.2307/1591036 ◽

1987 ◽

Vol 31 (4) ◽

pp. 809 ◽

Cited By ~ 7

Author(s):

A. Suwanichkul ◽

B. Panigrahy ◽

R. M. Wagner

Keyword(s):

Escherichia Coli ◽

Amino Acid ◽

Amino Acid Sequences ◽

Antigenic Relatedness

Download Full-text

The Primary Structure of Escherichia Coli RNA Polymerase. Nucleotide Sequences of the rpoB and rpoC Genes and Amino Acid Sequences of the β and β’ Subunits

Methods in Protein Sequence Analysis ◽

10.1007/978-1-4612-5832-2_29 ◽

1982 ◽

pp. 355-362

Author(s):

V. M. Lipkin ◽

E. D. Sverdlov ◽

G. S. Monastyrskaya ◽

Yu. A. Ovchinnikov

Keyword(s):

Escherichia Coli ◽

Amino Acid ◽

Rna Polymerase ◽

Primary Structure ◽

Nucleotide Sequences ◽

Amino Acid Sequences

Download Full-text

Purification and Characterization of the Recombinant Thermus sp. Strain T2 α-Galactosidase Expressed in Escherichia coli

Applied and Environmental Microbiology ◽

10.1128/aem.67.4.1601-1616.2001 ◽

2001 ◽

Vol 67 (4) ◽

pp. 1601-1606 ◽

Cited By ~ 31

Author(s):

Mitsunori Ishiguro ◽

Satoshi Kaneko ◽

Atsushi Kuno ◽

Yoshinori Koyama ◽

Shigeki Yoshida ◽

...

Keyword(s):

Escherichia Coli ◽

Amino Acid ◽

Polyacrylamide Gel Electrophoresis ◽

Active Form ◽

Gel Filtration ◽

Amino Acid Sequences ◽

Side Chain ◽

Catalytic Function ◽

Native Polyacrylamide Gel Electrophoresis

ABSTRACT The nucleotide sequence of the Thermus sp. strain T2 DNA coding for a thermostable α-galactosidase was determined. The deduced amino acid sequence of the enzyme predicts a polypeptide of 474 amino acids (M r, 53,514). The observed homology between the deduced amino acid sequences of the enzyme and α-galactosidase from Thermus brockianus was over 70%.Thermus sp. strain T2 α-galactosidase was expressed in its active form in Escherichia coli and purified. Native polyacrylamide gel electrophoresis and gel filtration chromatography data suggest that the enzyme is octameric. The enzyme was most active at 75°C forp-nitrophenyl-α-d-galactopyranoside hydrolysis, and it retained 50% of its initial activity after 1 h of incubation at 70°C. The enzyme was extremely stable over a broad range of pH (pH 6 to 13) after treatment at 40°C for 1 h. The enzyme acted on the terminal α-galactosyl residue, not on the side chain residue, of the galactomanno-oligosaccharides as well as those of yeasts and Mortierella vinacea α-galactosidase I. The enzyme has only one Cys residue in the molecule.para-Chloromercuribenzoic acid completely inhibited the enzyme but did not affect the mutant enzyme which contained Ala instead of Cys, indicating that this Cys residue is not responsible for its catalytic function.

Download Full-text

Subunit II (b') and Not Subunit I (b) of Photosynthetic ATP Synthases is Equivalent to Subunit b of the ATP Synthases from Nonphotosynthetic Eubacteria. Evidence for a New Assignment of b-Type F0 Subunits

Zeitschrift für Naturforschung C ◽

10.1515/znc-1997-11-1211 ◽

1997 ◽

Vol 52 (11-12) ◽

pp. 789-798 ◽

Cited By ~ 1

Author(s):

Hans-Jürgen Tiburzy ◽

Richard J. Berzborn

Keyword(s):

Escherichia Coli ◽

Amino Acid ◽

Structural Feature ◽

Atp Synthase ◽

Primary Structure ◽

Structural Features ◽

Amino Acid Sequences ◽

E Coli ◽

Subunit B ◽

Atp Synthases

Abstract Subunit I of chloroplast ATP synthase is reviewed until now to be equivalent to subunit b of Escherichia coli ATP synthase, whereas subunit II is suggested to be an additional subunit in photosynthetic ATP synthases lacking a counterpart in E. coli. After publication of some sequences of subunits II a revision of this assignment is necessary. Based on the analysis of 51 amino acid sequences of b-type subunits concerning similarities in primary structure, isoelectric point and a discovered discontinuous structural feature, our data provide evidence that chloroplast subunit II (subunit b' of photosynthetic eubacteria) and not chloroplast subunit I (subunit b of photosynthetic eubacteria) is the equivalent of subunit b of nonphoto synthetic eubacteria, and therefore does have a counterpart in e.g. E. coli. In consequence, structural features essential for function should be looked for on subunit II (b').

Download Full-text

Comparison of the structural and kinetic properties of the cytochrome c nitrite reductases from Escherichia coli, Wolinella succinogenes, Sulfurospirillum deleyianum and Desulfovibrio desulfuricans

Biochemical Society Transactions ◽

10.1042/bst0340143 ◽

2006 ◽

Vol 34 (1) ◽

pp. 143-145 ◽

Cited By ~ 17

Author(s):

T.A. Clarke ◽

A.M. Hemmings ◽

B. Burlat ◽

J.N. Butt ◽

J.A. Cole ◽

...

Keyword(s):

Escherichia Coli ◽

Amino Acid ◽

Active Site ◽

Desulfovibrio Desulfuricans ◽

Amino Acid Sequences ◽

Kinetic Properties ◽

Wolinella Succinogenes ◽

Nitrite Reductases ◽

Sulphite Reductase

The recent crystallographic characterization of NrfAs from Sulfurospirillum deleyianum, Wolinella succinogenes, Escherichia coli and Desulfovibrio desulfuricans allows structurally conserved regions to be identified. Comparison of nitrite and sulphite reductase activities from different bacteria shows that the relative activities vary according to organism. By comparison of both amino acid sequences and structures, differences can be identified in the monomer–monomer interface and the active-site channel; these differences could be responsible for the observed variance in substrate activity and indicate that subtle changes in the NrfA structure may optimize the enzyme for different roles.

Download Full-text