scholarly journals Enzymatic Properties of Dipeptidyl Aminopeptidase IV Produced by the Periodontal Pathogen Porphyromonas gingivalis and Its Participation in Virulence

2000 ◽  
Vol 68 (2) ◽  
pp. 716-724 ◽  
Author(s):  
Yumi Kumagai ◽  
Kiyoshi Konishi ◽  
Tomoharu Gomi ◽  
Hisao Yagishita ◽  
Ayako Yajima ◽  
...  
Keyword(s):  
Amino Acid ◽  
Porphyromonas Gingivalis ◽  
Catalytic Domain ◽  
Animal Experiments ◽  
Catalytic Triad ◽  
Amino Acid Sequences ◽  
Enzymatic Properties ◽  
Site Directed Mutagenesis ◽  
Periodontal Pathogen ◽  
Dipeptidyl Aminopeptidase

ABSTRACT Porphyromonas gingivalis is a major pathogen associated with adult periodontitis. We cloned and sequenced the gene (dpp) coding for dipeptidyl aminopeptidase IV (DPPIV) fromP. gingivalis W83, based on the amino acid sequences of peptide fragments derived from purified DPPIV. An Escherichia coli strain overproducing P. gingivalis DPPIV was constructed. The enzymatic properties of recombinant DPPIV purified from the overproducer were similar to those of DPPIV isolated fromP. gingivalis. The three amino acid residues Ser, Asp, and His, which are thought to form a catalytic triad in the C-terminal catalytic domain of eukaryotic DPPIV, are conserved in P. gingivalis DPPIV. When each of the corresponding residues of the enzyme was substituted with Ala by site-directed mutagenesis, DPPIV activity significantly decreased, suggesting that these three residues of P. gingivalis DPPIV are involved in the catalytic reaction. DPPIV-deficient mutants of P. gingivalis were constructed and subjected to animal experiments. Mice injected with the wild-type strain developed abscesses to a greater extent and died more frequently than those challenged with mutant strains. Mice injected with the mutants exhibited faster recovery from the infection, as assessed by weight gain and the rate of lesion healing. This decreased virulence of mutants compared with the parent strain suggests that DPPIV is a potential virulence factor of P. gingivalis and may play important roles in the pathogenesis of adult periodontitis induced by the organism.

scholarly journals Two Highly Similar Chitinases from Marine Vibrio Species have Different Enzymatic Properties

Marine Drugs ◽  
2020 ◽  
Vol 18 (3) ◽  
pp. 139
Author(s):  
Xinxin He ◽  
Min Yu ◽  
Yanhong Wu ◽  
Lingman Ran ◽  
Weizhi Liu ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Extracellular Enzymes ◽  
Vibrio Harveyi ◽  
Amino Acid Sequences ◽  
Enzymatic Properties ◽  
Site Directed Mutagenesis ◽  
Amino Acid Residues ◽  
Marine Vibrio ◽  
Key Sites

Chitinase, as one of the most important extracellular enzymes in the marine environment, has great ecological and applied values. In this study, two chitinases (Chi1557 and Chi4668) with 97.33% amino acid sequences identity were individually found in Vibrio rotiferianus and Vibrio harveyi. They both were encoding by 561 amino acids, but differed in 15 amino acids and showed different enzymatic properties. The optimal temperature and pH ranges were 45–50 °C and pH 5.0–7.0 for Chi1557, while ~50 °C and pH 3.0–6.0 for Chi4668. K+, Mg2+, and EDTA increased the enzymatic activity of Chi4668 significantly, yet these factors were inhibitory to Chi1557. Moreover, Chi1557 degraded colloidal chitin to produce (GlcNAc)2 and minor GlcNAc, whereas Chi4668 produce (GlcNAc)2 with minor (GlcNAc)3 and (GlcNAc)4. The Kcat/Km of Chi4668 was ~4.7 times higher than that of Chi1557, indicating that Chi4668 had stronger catalytic activity than Chi1557. Furthermore, site-directed mutagenesis was performed on Chi1557 focusing on seven conserved amino acid residues of family GH18 chitinases. Chi1557 was almost completely inactive after Glu154, Gln219, Tyr221, or Trp312 was individually mutated, retained ~50% activity after Tyr37 was mutated, and increased two times activity after Asp152 was mutated, indicating that these six amino acids were key sites for Chi1557.

scholarly journals Molecular Mechanism for Connective Tissue Destruction by Dipeptidyl Aminopeptidase IV Produced by the Periodontal Pathogen Porphyromonas gingivalis

2005 ◽  
Vol 73 (5) ◽  
pp. 2655-2664 ◽  
Author(s):  
Yumi Kumagai ◽  
Hisao Yagishita ◽  
Ayako Yajima ◽  
Tatsuya Okamoto ◽  
Kiyoshi Konishi
Keyword(s):  
Connective Tissue ◽  
Molecular Mechanism ◽  
Porphyromonas Gingivalis ◽  
Type I Collagen ◽  
Plasmid Vector ◽  
Periodontal Pathogen ◽  
Matrix Metalloproteinase 2 ◽  
Type I ◽  
Tissue Destruction ◽  
Dipeptidyl Aminopeptidase

ABSTRACT Porphyromonas gingivalis is a pathogen associated with adult periodontitis. It produces dipeptidyl aminopeptidase IV (DPPIV), which may act as a virulence factor by contributing to the degradation of connective tissue. We investigated the molecular mechanism by which DPPIV contributes to the destruction of connective tissue. DPPIV itself did not show gelatinase or collagenase activity toward human type I collagen, but it promoted the activity of the host-derived matrix metalloproteinase 2 (MMP-2) (gelatinase) and MMP-1 (collagenase). DPPIV bound to fibronectin and mediated the adhesion of P. gingivalis to fibronectin. Mutant DPPIV with catalytic Ser mutagenized to Ala (DPPSA) did not accelerate the degradation of collagen and gelatin by MMPs but retained fibronectin-binding activity. The adhesion of human gingival fibroblasts and NIH 3T3 cells to fibronectin was inhibited by DPPIV. Strain 4351ADPPSA exhibited an intermediate level of virulence in mice, between that of the strain expressing wild-type DPPIV (4351ADPP) and that of the strain harboring only the plasmid vector (4351AVEC). It is suggested that both activity promoting the degradation of collagen and gelatin and binding to fibronectin are required for full virulence. These results reveal novel biological functions of DPPIV and suggest a pathological role in the progression of periodontitis.

Enzymatic Properties and Nucleotide and Amino Acid Sequences of a Thermostable β-Agarase from the Novel Marine Isolate, JAMB-A94

2004 ◽  
Vol 68 (5) ◽  
pp. 1073-1081 ◽  
Author(s):  
Yukari OHTA ◽  
Yuichi NOGI ◽  
Masayuki MIYAZAKI ◽  
Zhijun LI ◽  
Yuji HATADA ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Enzymatic Properties ◽  
The Novel ◽  
Marine Isolate

Activity modulation of the oligopeptidase B from Serratia proteamaculans by site-directed mutagenesis of amino acid residues surrounding catalytic triad histidine

Biochimie ◽  
2017 ◽  
Vol 139 ◽  
pp. 125-136 ◽  
Author(s):  
Anna G. Mikhailova ◽  
Tatiana V. Rakitina ◽  
Vladimir I. Timofeev ◽  
David M. Karlinsky ◽  
Dmitry A. Korzhenevskiy ◽  
...  
Keyword(s):  
Amino Acid ◽  
Catalytic Triad ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Amino Acid Residues ◽  
Serratia Proteamaculans ◽  
Oligopeptidase B

scholarly journals Protein engineering of the 2-haloacid halidohydrolase IVa from Pseudomonas cepacia MBA4

1993 ◽  
Vol 292 (1) ◽  
pp. 69-74 ◽  
Author(s):  
W Asmara ◽  
U Murdiyatmo ◽  
A J Baines ◽  
A T Bull ◽  
D J Hardman
Keyword(s):  
Amino Acid ◽  
Rational Design ◽  
Catalytic Mechanism ◽  
Protonated Form ◽  
Amino Acid Sequences ◽  
Site Directed Mutagenesis ◽  
Pseudomonas Cepacia ◽  
Amino Acid Residues ◽  
Substrate Complex ◽  
Key Residues

The chemical modification of L-2-haloacid halidohydrolase IVa (Hdl IVa), originally identified in Pseudomonas cepacia MBA4, produced as a recombinant protein in Escherichia coli DH5 alpha, led to the identification of histidine and arginine as amino acid residues likely to play a part in the catalytic mechanism of the enzyme. These results, together with DNA sequence and analyses [Murdiyatmo, Asmara, Baines, Bull and Hardman (1992) Biochem. J. 284, 87-93] provided the basis for the rational design of a series of random- and site-directed-mutagenesis experiments of the Hdl IVa structural gene (hdl IVa). Subsequent apparent kinetic analyses of purified mutant enzymes identified His-20 and Arg-42 as the key residues in the activity of this halidohydrolase. It is also proposed that Asp-18 is implicated in the functioning of the enzyme, possibly by positioning the correct tautomer of His-20 for catalysis in the enzyme-substrate complex and stabilizing the protonated form of His-20 in the transition-state complex. Comparison of conserved amino acid sequences between the Hdl IVa and other halidohydrolases suggests that L-2-haloacid halidohydrolases contain conserved amino acid sequences that are not found in halidohydrolases active towards both D- and L-2-monochloropropionate.

scholarly journals Identification and Characterization of Porphyromonas gingivalis Client Proteins That Bind to Streptococcus oralis Glyceraldehyde-3-Phosphate Dehydrogenase

2012 ◽  
Vol 81 (3) ◽  
pp. 753-763 ◽  
Author(s):  
Kazuhiko Maeda ◽  
Hideki Nagata ◽  
Masae Kuboniwa ◽  
Miki Ojima ◽  
Tsukasa Osaki ◽  
...  
Keyword(s):  
Amino Acid ◽  
Porphyromonas Gingivalis ◽  
Interaction Analysis ◽  
Site Directed Mutagenesis ◽  
Receptor Protein ◽  
Oral Streptococci ◽  
Amino Acid Residues ◽  
Content Type ◽  
Streptococcus Oralis ◽  
Client Proteins

ABSTRACTCoaggregation ofPorphyromonas gingivalisand oral streptococci is thought to play an important role inP. gingivaliscolonization. Previously, we reported thatP. gingivalismajor fimbriae interacted withStreptococcus oralisglyceraldehyde-3-phosphate dehydrogenase (GAPDH), and that amino acid residues 166 to 183 of GAPDH exhibited strong binding activity towardP. gingivalisfimbriae (H. Nagata, M. Iwasaki, K. Maeda, M. Kuboniwa, E. Hashino, M. Toe, N. Minamino, H. Kuwahara, and S. Shizukuishi, Infect. Immun.77:5130–5138, 2009). The present study aimed to identify and characterizeP. gingivaliscomponents other than fimbriae that interact withS. oralisGAPDH. A pulldown assay was performed to detect potential interactions betweenP. gingivalisclient proteins andS. oralisrecombinant GAPDH with amino acid residues 166 to 183 deleted by site-directed mutagenesis. Seven proteins, namely,tonB-dependent receptor protein (RagA4), arginine-specific proteinase B, 4-hydroxybutyryl-coenzyme A dehydratase (AbfD), lysine-specific proteinase, GAPDH, NAD-dependent glutamate dehydrogenase (GDH), and malate dehydrogenase (MDH), were identified by two-dimensional gel electrophoresis followed by proteomic analysis using tandem mass spectrometry. Interactions between these client proteins andS. oralisGAPDH were analyzed with a biomolecular interaction analysis system.S. oralisGAPDH showed high affinity for five of the seven client proteins (RagA4, AbfD, GAPDH, GDH, and MDH). Interactions betweenP. gingivalisandS. oraliswere measured by a turbidimetric method and fluorescence microscopy. RagA4, AbfD, and GDH enhanced coaggregation, whereas GAPDH and MDH inhibited coaggregation. Furthermore, the expression ofluxSinP. gingivaliswas upregulated by RagA4, AbfD, and GDH but was downregulated by MDH. These results indicate that the fiveP. gingivalisclient proteins function as regulators inP. gingivalisbiofilm formation with oral streptococci.

Directed evolution to produce an alkalophilic variant from a Neocallimastix patriciarum xylanase

2001 ◽  
Vol 47 (12) ◽  
pp. 1088-1094 ◽  
Author(s):  
Yew-Loom Chen ◽  
Tsung-Yin Tang ◽  
Kuo-Joan Cheng
Keyword(s):  
Amino Acid ◽  
Directed Evolution ◽  
Catalytic Domain ◽  
Specific Activity ◽  
Synergistic Effects ◽  
High Specific Activity ◽  
Site Directed Mutagenesis ◽  
Amino Acid Substitutions ◽  
Wild Type ◽  
Neocallimastix Patriciarum

The catalytic domain of a xylanase from the anaerobic fungus Neocallimastix patriciarum was made more alkalophilic through directed evolution using error-prone PCR. Transformants expressing the alkalophilic variant xylanases produced larger clear zones when overlaid with high pH, xylan-containing agar. Eight amino acid substitutions were identified in six selected mutant xylanases. Whereas the wild-type xylanase exhibited no activity at pH 8.5, the relative and specific activities of the six mutants were higher at pH 8.5 than at pH 6.0. Seven of the eight amino acid substitutions were assembled in one enzyme (xyn-CDBFV) by site-directed mutagenesis. Some or all of the seven mutations exerted positive and possibly synergistic effects on the alkalophilicity of the enzyme. The resulting composite mutant xylanase retained a greater proportion of its activity than did the wild type at pH above 7.0, maintaining 25% of its activity at pH 9.0, and its retention of activity at acid pH was no lower than that of the wild type. The composite xylanase (xyn-CDBFV) had a relatively high specific activity of 10 128 µmol glucose·min–1·(mg protein)–1 at pH 6.0. It was more thermostable at 60°C and alkaline tolerant at pH 10.0 than the wild-type xylanase. These properties suggest that the composite mutant xylanase is a promising and suitable candidate for paper pulp bio-bleaching.Key words: xylanase, Neocallimastix patriciarum, alkalophilicity, random mutagenesis, directed evolution.

scholarly journals Characterization of a Thermoacidophilic l-Arabinose Isomerase from Alicyclobacillus acidocaldarius: Role of Lys-269 in pH Optimum

2005 ◽  
Vol 71 (12) ◽  
pp. 7888-7896 ◽  
Author(s):  
Sang-Jae Lee ◽  
Dong-Woo Lee ◽  
Eun-Ah Choe ◽  
Young-Ho Hong ◽  
Seong-Bo Kim ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Site Directed Mutagenesis ◽  
Bacillus Halodurans ◽  
Wild Type ◽  
Ph Optimum ◽  
Calculated Molecular Mass ◽  
Alicyclobacillus Acidocaldarius ◽  
Arabinose Isomerase

ABSTRACT The araA gene encoding l-arabinose isomerase (AI) from the thermoacidophilic bacterium Alicyclobacillus acidocaldarius was cloned, sequenced, and expressed in Escherichia coli. Analysis of the sequence revealed that the open reading frame of the araA gene consists of 1,491 bp that encodes a protein of 497 amino acid residues with a calculated molecular mass of 56,043 Da. Comparison of the deduced amino acid sequence of A. acidocaldarius AI (AAAI) with other AIs demonstrated that AAAI has 97% and 66% identities (99% and 83% similarities) to Geobacillus stearothermophilus AI (GSAI) and Bacillus halodurans AI (BHAI), respectively. The recombinant AAAI was purified to homogeneity by heat treatment, ion-exchange chromatography, and gel filtration. The purified enzyme showed maximal activity at pH 6.0 to 6.5 and 65°C under the assay conditions used, and it required divalent cations such as Mn2+, Co2+, and Mg2+ for its activity. The isoelectric point (pI) of the enzyme was about 5.0 (calculated pI of 5.5). The apparent Km values of the recombinant AAAI for l-arabinose and d-galactose were 48.0 mM (V max, 35.5 U/mg) and 129 mM (V max, 7.5 U/mg), respectively, at pH 6 and 65°C. Interestingly, although the biochemical properties of AAAI are quite similar to those of GSAI and BHAI, the three AIs from A. acidocaldarius (pH 6), G. stearothermophilus (pH 7), and B. halodurans (pH 8) exhibited different pH activity profiles. Based on alignment of the amino acid sequences of these homologous AIs, we propose that the Lys-269 residue of AAAI may be responsible for the ability of the enzyme to act at low pH. To verify the role of Lys-269, we prepared the mutants AAAI-K269E and BHAI-E268K by site-directed mutagenesis and compared their kinetic parameters with those of wild-type AIs at various pHs. The pH optima of both AAAI-K269E and BHAI-E268K were rendered by 1.0 units (pH 6 to 7 and 8 to 7, respectively) compared to the wild-type enzymes. In addition, the catalytic efficiency (k cat/Km ) of each mutant at different pHs was significantly affected by an increase or decrease in V max. From these results, we propose that the position corresponding to the Lys-269 residue of AAAI could play an important role in the determination of the pH optima of homologous AIs.

scholarly journals iSulfoTyr-PseAAC: Identify Tyrosine Sulfation Sites by Incorporating Statistical Moments via Chou’s 5-steps Rule and Pseudo Components

2019 ◽  
Vol 20 (4) ◽  
pp. 306-320 ◽  
Author(s):  
Omar Barukab ◽  
Yaser Daanial Khan ◽  
Sher Afzal Khan ◽  
Kuo-Chen Chou
Keyword(s):  
Amino Acid ◽  
Computational Model ◽  
Amino Acid Sequences ◽  
Site Directed Mutagenesis ◽  
Statistical Moments ◽  
Amino Acid Residues ◽  
Tyrosine Sulfation ◽  
Protein Amino Acid ◽  
Jackknife Test ◽  
Self Consistency

Background: The amino acid residues, in protein, undergo post-translation modification (PTM) during protein synthesis, a process of chemical and physical change in an amino acid that in turn alters behavioral properties of proteins. Tyrosine sulfation is a ubiquitous posttranslational modification which is known to be associated with regulation of various biological functions and pathological processes. Thus its identification is necessary to understand its mechanism. Experimental determination through site-directed mutagenesis and high throughput mass spectrometry is a costly and time taking process, thus, the reliable computational model is required for identification of sulfotyrosine sites. Methodology: In this paper, we present a computational model for the prediction of the sulfotyrosine sites named iSulfoTyr-PseAAC in which feature vectors are constructed using statistical moments of protein amino acid sequences and various position/composition relative features. These features are incorporated into PseAAC. The model is validated by jackknife, cross-validation, self-consistency and independent testing. Results: Accuracy determined through validation was 93.93% for jackknife test, 95.16% for crossvalidation, 94.3% for self-consistency and 94.3% for independent testing. Conclusion: The proposed model has better performance as compared to the existing predictors, however, the accuracy can be improved further, in future, due to increasing number of sulfotyrosine sites in proteins.

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