scholarly journals Identification and biochemical characterization of two novel UDP-2,3-diacetamido-2,3-dideoxy-α-D-glucuronic acid 2-epimerases from respiratory pathogens

2007 ◽  
Vol 405 (1) ◽  
pp. 123-130 ◽  
Author(s):  
Erin L. Westman ◽  
David J. Mcnally ◽  
Martin Rejzek ◽  
Wayne L. Miller ◽  
Vellupillai Sri Kannathasan ◽  
...  
Keyword(s):  
Capillary Electrophoresis ◽  
Glucuronic Acid ◽  
Biochemical Characterization ◽  
Intermediate Compound ◽  
Proton Spectrum ◽  
Respiratory Pathogens ◽  
Sodium Phosphate Buffer ◽  
Mannuronic Acid ◽  
Enzyme Substrate

The heteropolymeric O-antigen of the lipopolysaccharide from Pseudomonas aeruginosa serogroup O5 as well as the band-A trisaccharide from Bordetella pertussis contain the di-N-acetylated mannosaminuronic acid derivative, β-D-ManNAc3NAcA (2,3-diacetamido-2,3-dideoxy-β-D-mannuronic acid). The biosynthesis of the precursor for this sugar is proposed to require five steps, through which UDP-α-D-GlcNAc (UDP-N-acetyl-α-D-glucosamine) is converted via four steps into UDP-α-D-GlcNAc3NAcA (UDP-2,3-diacetamido-2,3-dideoxy-α-D-glucuronic acid), and this intermediate compound is then epimerized by WbpI (P. aeruginosa), or by its orthologue, WlbD (B. pertussis), to form UDP-α-D-ManNAc3NAcA (UDP-2,3-diacetamido-2,3-dideoxy-α-D-mannuronic acid). UDP-α-D-GlcNAc3NAcA, the proposed substrate for WbpI and WlbD, was obtained through chemical synthesis. His6–WbpI and His6–WlbD were overexpressed and then purified by affinity chromatography using FPLC. Capillary electrophoresis was used to analyse reactions with each enzyme, and revealed that both enzymes used UDP-α-D-GlcNAc3NAcA as a substrate, and reacted optimally in sodium phosphate buffer (pH 6.0). Neither enzyme utilized UDP-α-D-GlcNAc, UDP-α-D-GlcNAcA (UDP-2-acetamido-2,3-dideoxy-α-D-glucuronic acid) or UDP-α-D-GlcNAc3NAc (UDP-2,3-diacetamido-2,3-dideoxy-α-D-glucose) as substrates. His6–WbpI or His6–WlbD reactions with UDP-α-D-GlcNAc3NAcA produce a novel peak with an identical retention time, as shown by capillary electrophoresis. To unambiguously characterize the reaction product, enzyme–substrate reactions were allowed to proceed directly in the NMR tube and conversion of substrate into product was monitored over time through the acquisition of a proton spectrum at regular intervals. Data collected from one- and two-dimensional NMR experiments showed that His6–WbpI catalysed the 2-epimerization of UDP-α-D-GlcNAc3NAcA, converting it into UDP-α-D-ManNAc3NAcA. Collectively, these results provide evidence that WbpI and WlbD are UDP-2,3-diacetamido-2,3-dideoxy-α-D-glucuronic acid 2-epimerases.

Identification and biochemical characterization of two novel UDP-2,3-diacetamido-2,3-dideoxy-α-D-glucuronic acid 2-epimerases from respiratory pathogens

2007 ◽  
Vol 405 (3) ◽  
pp. 625-625
Author(s):  
E. L. Westman ◽  
D. J. Mcnally ◽  
M. Rejzek ◽  
W. L. Miller ◽  
V. S. Kannathasan ◽  
...  
Keyword(s):  
Glucuronic Acid ◽  
Biochemical Characterization ◽  
Respiratory Pathogens

scholarly journals Biochemical characterization of a novel ulvan lyase from Pseudoalteromonas sp. strain PLSV

RSC Advances ◽  
2018 ◽  
Vol 8 (5) ◽  
pp. 2610-2615 ◽  
Author(s):  
Hui-Min Qin ◽  
Panpan Xu ◽  
Qianqian Guo ◽  
Xiaotao Cheng ◽  
Dengke Gao ◽  
...  
Keyword(s):  
Cell Wall ◽  
Glucuronic Acid ◽  
Biochemical Characterization ◽  
Iduronic Acid ◽  
Green Seaweed

Ulvans, complex polysaccharides found in the ulvales (green seaweed) cell wall, contain predominantly 3-sulfated rhamnose (Rha3S) linked to either d-glucuronic acid, l-iduronic acid or d-xylose.

scholarly journals Biochemical characterization of the chondroitinase ABC I active site

2005 ◽  
Vol 390 (2) ◽  
pp. 395-405 ◽  
Author(s):  
Vikas Prabhakar ◽  
Rahul Raman ◽  
Ishan Capila ◽  
Carlos J. Bosques ◽  
Kevin Pojasek ◽  
...  
Keyword(s):  
Active Site ◽  
Structural Model ◽  
Catalytic Mechanism ◽  
Biochemical Characterization ◽  
Chondroitin Sulphate ◽  
Critical Role ◽  
Site Directed Mutagenesis ◽  
Chondroitinase Abc ◽  
Enzyme Substrate

cABC I (chondroitinase ABC I) from Proteus vulgaris is a GalAG (galactosaminoglycan) depolymerizing lyase that cleaves its substrates at the glycosidic bond via β-elimination. cABC I cleaves a particularly broad range of GalAG substrates, including CS (chondroitin sulphate), DS (dermatan sulphate) and hyaluronic acid. We recently cloned and recombinantly expressed cABC I in Escherichia coli, and completed a preliminary biochemical characterization of the enzyme. In the present study, we have coupled site-directed mutagenesis of the recombinant cABC I with a structural model of the enzyme–substrate complex in order to investigate in detail the roles of active site amino acids in the catalytic action of the enzyme. The putative catalytic residues His-501, Tyr-508, Arg-560 and Glu-653 were probed systematically via mutagenesis. Assessment of these mutants in kinetic and end-point assays provided direct evidence on the catalytic roles of these active-site residues. The crystal structure of the native enzyme provided a framework for molecular docking of representative CS and DS substrates. This enabled us to construct recombinant enzyme–substrate structural complexes. These studies together provided structural insights into the effects of the mutations on the catalytic mechanism of cABC I and the differences in its processing of CS and DS substrates. All His-501 mutants were essentially inactive and thereby implicating this amino acid to play the critical role of proton abstraction during catalysis. The kinetic data for Glu-653 mutants indicated that it is involved in a hydrogen bonding network in the active site. The proximity of Tyr-508 to the glycosidic oxygen of the substrate at the site of cleavage suggested its potential role in protonating the leaving group. Arg-560 was proximal to the uronic acid C-5 proton, suggesting its possible role in the stabilization of the carbanion intermediate formed during catalysis.

Biochemical characterization of the β-1,4-glucuronosyltransferase GelK in the gellan gum-producing strain Sphingomonas paucimobilis A.T.C.C. 31461

2001 ◽  
Vol 358 (2) ◽  
pp. 457-464 ◽  
Author(s):  
Paula VIDEIRA ◽  
Arsénio FIALHO ◽  
Roberto A. GEREMIA ◽  
Christelle BRETON ◽  
Isabel SÁ-CORREIA
Keyword(s):  
Glucuronic Acid ◽  
Biochemical Characterization ◽  
Sequence Similarity ◽  
Enzymic Activity ◽  
Gellan Gum ◽  
Open Reading Frames ◽  
Sphingomonas Paucimobilis ◽  
E Coli ◽  
Repeat Units

Biosynthesis of bacterial polysaccharide-repeat units proceeds by sequential transfer of sugars, from the appropriate sugar donor to an activated lipid carrier, by committed glycosyltransferases (GTs). Few studies on the mechanism of action for this type of GT are available. Sphingomonas paucimobilis A.T.C.C. 31461 produces the industrially important polysaccharide gellan gum. We have cloned the gelK gene from S. paucimobilis A.T.C.C. 31461. GelK belongs to family 1 of the GT classification [Campbell, Davies, Bulone, Henrissat (1997) Biochem. J. 326, 929–939]. Sequence similarity studies suggest that GelK consists of two protein modules corresponding to the -NH2 and -CO2H halves, the latter possibly harbouring the GT activity. The gelK gene and the open reading frames coding for the -NH2 (GelKNH2) and -CO2H (GelKCOOH) halves were overexpressed in Escherichia coli. GelK and GelKNH2 were present in both the soluble and membrane fractions of E. coli, whereas GelKCOOH was only present in the soluble fraction. GelK catalysed the transfer of [14C]glucuronic acid from UDP-[14C]glucuronic acid into a glycolipid extracted from S. paucimobilis or E. coli, even in the presence of EDTA, and the radioactive sugar was released from the glycolipid by β-1,4-glucuronidase. GelK was not able to use synthetic glucosyl derivatives as acceptors, indicating that the PPi-lipid moiety is needed for enzymic activity. Recombinant GelKNH2 and GelKCOOH did not show detectable activity. Based on the biochemical characteristics of GelK and on sequence similarities with N-acetylglucosaminyltransferase, we propose that GT families 1 and 28 form a superfamily.

Plant Pathology Diagnosed by X-Ray Microanalysis

1987 ◽  
Vol 45 ◽  
pp. 974-975
Author(s):  
J. H. Resau ◽  
N. Howell ◽  
S. H. Chang
Keyword(s):  
Electron Microscopy ◽  
Plant Pathology ◽  
Biochemical Characterization ◽  
Nutrient Deficiency ◽  
Green Leaf ◽  
Parasitic Infestation ◽  
X Ray

Spinach grown in Texas developed “yellow spotting” on the peripheral portions of the leaves. The exact cause of the discoloration could not be determined as there was no evidence of viral or parasitic infestation of the plants and biochemical characterization of the plants did not indicate any significant differences between the yellow and green leaf portions of the spinach. The present study was undertaken using electron microscopy (EM) to determine if a micro-nutrient deficiency was the cause for the discoloration.Green leaf spinach was collected from the field and sent by express mail to the EM laboratory. The yellow and equivalent green portions of the leaves were isolated and dried in a Denton evaporator at 10-5 Torr for 24 hrs. The leaf specimens were then examined using a JEOL 100 CX analytical microscope. TEM specimens were prepared according to the methods of Trump et al.

Interaction effect of rootstocks on gas exchange parameters, biochemical changes and nutrientstatus in Sauvignon Blanc winegrapes

2014 ◽  
Vol 3 (3) ◽  
pp. 218-225
Author(s):  
R. G. Somkuwar ◽  
M. A. Bhange ◽  
A. K. Upadhyay ◽  
S. D. Ramteke
Keyword(s):  
Biochemical Characterization ◽  
Reducing Sugar ◽  
Wine Grape ◽  
Gas Exchange Parameters ◽  
Food Material ◽  
Total Carbohydrates ◽  
Salt Creek ◽  
Grape Varieties ◽  
Photosynthetic Activities

SauvignonBlanc wine grape was characterized for their various morphological, physiological and biochemical parameters grafted on different rootstocks. Significant differences were recorded for all the parameters studied. The studies on vegetative parameters revealed that the rootstock influences the vegetative growth thereby increasing the photosynthetic activities of a vine. The highest photosynthesis rate was recorded in 140-Ru grafted vine followed by Fercal whereas the lowest in Salt Creek rootstock grafted vines.The rootstock influenced the changes in biochemical constituents in the grafted vine thereby helping the plant to store enough food material. Significant differences were recorded for total carbohydrates, proteins, total phenols and reducing sugar. The vines grafted on1103-Pshowed highest carbohydrates and starch followed by 140-Ru,while the least amount of carbohydrates were recorded in 110-R and Salt Creek grafted vines respectively.Among the different rootstock graft combinations, Fercal showed highest amount of reducing sugar, proteins and phenols, followed by 1103-P and SO4, however, the lowest amount of reducing sugar, proteins and phenols were recorded with 110-R grafted vines.The vines grafted on different rootstocks showed changes in nutrient uptake. Considering this, the physico-biochemical characterization of grafted vine may help to identify particularrootstocks combination that could influence a desired trait in commercial wine grape varieties after grafting.

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