scholarly journals Identification and characterization of DdPDE3, a cGMP-selective phosphodiesterase from Dictyostelium

2001 ◽  
Vol 353 (3) ◽  
pp. 635-644 ◽  
Author(s):  
Hidekazu KUWAYAMA ◽  
Helena SNIPPE ◽  
Mari DERKS ◽  
Jeroen ROELOFS ◽  
Peter J. M. VAN HAASTERT
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Catalytic Domain ◽  
Expressed Sequence Tag ◽  
Sequence Similarity ◽  
Second Messengers ◽  
Kinetic Properties ◽  
Intracellular Camp ◽  
Catalytic Domains ◽  
Dual Specificity

In Dictyostelium cAMP and cGMP have important functions as first and second messengers in chemotaxis and development. Two cyclic-nucleotide phosphodiesterases (DdPDE 1 and 2) have been identified previously, an extracellular dual-specificity enzyme and an intracellular cAMP-specific enzyme (encoded by the psdA and regA genes respectively). Biochemical data suggest the presence of at least one cGMP-specific phosphodiesterase (PDE) that is activated by cGMP. Using bioinformatics we identified a partial sequence in the Dictyostelium expressed sequence tag database that shows a high degree of amino acid sequence identity with mammalian PDE catalytic domains (DdPDE3). The deduced amino acid sequence of a full-length DdPDE3 cDNA isolated in this study predicts a 60kDa protein with a 300-residue C-terminal PDE catalytic domain, which is preceded by approx. 200 residues rich in asparagine and glutamine residues. Expression of the DdPDE3 catalytic domain in Escherichia coli shows that the enzyme has Michaelis–Menten kinetics and a higher affinity for cGMP (Km = 0.22µM) than for cAMP (Km = 145µM); cGMP does not stimulate enzyme activity. The enzyme requires bivalent cations for activity; Mn2+ is preferred to Mg2+, whereas Ca2+ yields no activity. DdPDE3 is inhibited by 3-isobutyl-1-methylxanthine with an IC50 of approx. 60µM. Overexpression of the DdPDE3 catalytic domain in Dictyostelium confirms these kinetic properties without indications of its activation by cGMP. The properties of DdPDE3 resemble those of mammalian PDE9, which also shows the highest sequence similarity within the catalytic domains. DdPDE3 is the first cGMP-selective PDE identified in lower eukaryotes.

scholarly journals In silico characterization and expression analyses of sugarcane putative sucrose non-fermenting-1 (SNF1) related kinases

2001 ◽  
Vol 24 (1-4) ◽  
pp. 35-41 ◽  
Author(s):  
Dirce Maria Carraro ◽  
Marcio R. Lambais ◽  
Helaine Carrer
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Protein Kinases ◽  
Catalytic Domain ◽  
Expressed Sequence Tag ◽  
Higher Plants ◽  
Expression Patterns ◽  
Amino Acid Sequences ◽  
Cdna Libraries ◽  
Expressed Sequence

Sucrose non-fermenting-1-related protein kinases (SnRKs) may play a major role in regulating gene expression in plant cells. This family of regulatory proteins is represented by sucrose non-fermenting-1 (SNF1) protein kinase in Saccharomyces cerevisiae, AMP-activated protein kinases (AMPKs) in mammals and SnRKs in higher plants. The SnRK family has been reorganized into three subfamilies according to the evolutionary relationships of their amino acid sequences. Members of the SnRK subfamily have been identified in several plants. There is evidence that they are involved in the nutritional and/or environmental stress response, although their roles are not yet well understood. We have identified at least 22 sugarcane expressed sequence tag (EST) contigs encoding putative SnRKs. The amino acid sequence alignment of both putative sugarcane SnRKs and known SnRKs revealed a highly conserved N-terminal catalytic domain. Our results indicated that sugarcane has at least one member of each SnRK subfamily. Expression pattern analysis of sugarcane EST-contigs encoding putative SnRKs in 26 selected cDNA libraries from the sugarcane expressed sequence tag SUCEST database has indicated that members of this family are expressed throughout the plant. Members of the same subfamily showed no specific expression patterns, suggesting that their functions are not related to their phylogenic relationships based on N-terminal amino acid sequence phylogenetic relationships.

scholarly journals The characterization of a cyclophilin-type peptidyl prolyl cis-trans-isomerase from the endoplasmic-reticulum lumen

1994 ◽  
Vol 300 (3) ◽  
pp. 871-875 ◽  
Author(s):  
S Bose ◽  
M Mücke ◽  
R B Freedman
Keyword(s):  
Endoplasmic Reticulum ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Sequence Similarity ◽  
Liver Microsomes ◽  
Bovine Liver ◽  
Kinetic Properties ◽  
Cyclophilin B ◽  
Strong Sequence Similarity

A luminally located peptidyl prolyl cis-trans-isomerase (PPI) has been purified from bovine liver microsomes. It has a molecular mass of 20.6 kDa, and N-terminal sequencing demonstrates strong sequence similarity to the sequences of the cyclophilin B family. The enzyme catalyses the isomerization of the standard proline-containing peptide N-succinyl-Ala-Ala-Pro-Phe p-nitroanilide, as well as the refolding of RNAase T1. Kinetic properties, substrate-specificity data and inhibition by cyclosporin A indicate that it is a cyclophilin-type PPI, consistent with the amino-acid-sequence results.

scholarly journals Analysis of Htra Gene from Zebrafish (Danio Rerio)

2015 ◽  
Vol 10 (2) ◽  
Author(s):  
M. Murwantoko ◽  
Chio Oka ◽  
Masashi Kawaichi
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Danio Rerio ◽  
Serine Proteases ◽  
Catalytic Domain ◽  
Fruit Fly ◽  
Wide Range ◽  
Igf Binding ◽  
Bacterial Homolog

HtrA which is characterized by the combination of a trypsin-like catalytic domain with at least one C-terminalPDZ domain is a highly conserved family of serine proteases found in a wide range of organisms. However theidentified HtrA family numbers varies among spesies, for example the number of mammalian, Eschericia coli,fruit fly-HtrA family are 4, 3 and 1 gene respectively. One gene is predicted exist in zebrafish. Since no completeinformation available on zebrafish HtrA, in this paper zebrafish HtrA (zHtrA) gene was analyzed. The zHtrA isbelonged to HtrA1 member and predicted encodes 478 amino acids with a signal peptide, a IGF binding domain,a Kazal-type inhibitor domain in the up stream of HtrA-bacterial homolog. At the amino acid sequence the zHtrA1showed the 69%, 69%, 68%, 54% and 54% with the rat HtrA1, mouse HtrA1, human HtrA1, human HtrA3 andmouse HtrA4 respectively. The zHtrA1 is firstly expressed at 60 hpf and mainly in the vertebral rudiments in thetail region.

scholarly journals Engineered Resistance Against Papaya ringspot virus in Venezuelan Transgenic Papayas

Plant Disease ◽  
2004 ◽  
Vol 88 (5) ◽  
pp. 516-522 ◽  
Author(s):  
Gustavo Fermin ◽  
Valentina Inglessis ◽  
Cesar Garboza ◽  
Sairo Rangel ◽  
Manuel Dagert ◽  
...  
Keyword(s):  
Amino Acid ◽  
Agrobacterium Tumefaciens ◽  
Coat Protein ◽  
Amino Acid Sequence ◽  
Sequence Similarity ◽  
Ringspot Virus ◽  
Amino Acid Sequence Similarity ◽  
Papaya Ringspot Virus ◽  
Local Varieties ◽  
Cp Gene

Local varieties of papaya grown in the Andean foothills of Mérida, Venezuela, were transformed independently with the coat protein (CP) gene from two different geographical Papaya ringspot virus (PRSV) isolates, designated VE and LA, via Agrobacterium tumefaciens. The CP genes of both PRSV isolates show 92 and 96% nucleotide and amino acid sequence similarity, respectively. Four PRSV-resistant R0 plants were intercrossed or selfed, and the progenies were tested for resistance against the homologous isolates VE and LA, and the heterologous isolates HA (Hawaii) and TH (Thailand) in greenhouse conditions. Resistance was affected by sequence similarity between the transgenes and the challenge viruses: resistance values were higher for plants challenged with the homologous isolates (92 to 100% similarity) than with the Hawaiian (94% similarity) and, lastly, Thailand isolates (88 to 89% similarity). Our results show that PRSV CP gene effectively protects local varieties of papaya against homologous and heterologous isolates of PRSV.

scholarly journals Structural gene and complete amino acid sequence of Vibrio alginolyticus collagenase

1992 ◽  
Vol 281 (3) ◽  
pp. 703-708 ◽  
Author(s):  
H Takeuchi ◽  
Y Shibano ◽  
K Morihara ◽  
J Fukushima ◽  
S Inami ◽  
...  
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Amino Acid Sequence ◽  
Structural Gene ◽  
Sequence Similarity ◽  
Vibrio Alginolyticus ◽  
Amino Acid Sequences ◽  
Dna Encoding ◽  
Cloned Gene ◽  
Collagenase Gene

The DNA encoding the collagenase of Vibrio alginolyticus was cloned, and its complete nucleotide sequence was determined. When the cloned gene was ligated to pUC18, the Escherichia coli expression vector, bacteria carrying the gene exhibited both collagenase antigen and collagenase activity. The open reading frame from the ATG initiation codon was 2442 bp in length for the collagenase structural gene. The amino acid sequence, deduced from the nucleotide sequence, revealed that the mature collagenase consists of 739 amino acids with an Mr of 81875. The amino acid sequences of 20 polypeptide fragments were completely identical with the deduced amino acid sequences of the collagenase gene. The amino acid composition predicted from the DNA sequence was similar to the chemically determined composition of purified collagenase reported previously. The analyses of both the DNA and amino acid sequences of the collagenase gene were rigorously performed, but we could not detect any significant sequence similarity to other collagenases.

scholarly journals Human diadenosine 5′,5′′′-P1,P4-tetraphosphate pyrophosphohydrolase is a member of the MutT family of nucleotide pyrophosphatases

1995 ◽  
Vol 311 (3) ◽  
pp. 717-721 ◽  
Author(s):  
N M H Thorne ◽  
S Hankin ◽  
M C Wilkinson ◽  
C Nuñez ◽  
R Barraclough ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Expressed Sequence Tag ◽  
Sequence Motif ◽  
Diadenosine Tetraphosphate ◽  
Expressed Sequence

The cDNA and derived amino acid sequence of human diadenosine 5′,5‴-P1,P4-tetraphosphate pyrophosphohydrolase have been determined with the aid of the GenBank Expressed Sequence Tag database. This enzyme possesses a modification of the MutT sequence motif found in certain nucleotide pyrophosphatases. It is unrelated to the enzymes of diadenosine tetraphosphate catabolism found in prokaryotes and fungi.

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