3D-sturctures of Lactate Dehydrogenase from 4 Lactic Acid Bacteria predicted by Comparative Modeling Tool
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Output of the 3D-structures modeled by comparative modeling tool for LDH enzymes from four LABs (in the PDB format, tarred). Four LABs include Enterococcus faecalis, Lactococcus lactis, Streptococcus pyogenes and Lactobacillus plantarum. Output of the SEEK Model https://seek.sysmo-db.org/models/118.
The modeling was performed against a x-ray structure of LDH from B. stearothermophilis (template, PDH ID: 1LDN).
FAIRDOMHub ID: https://fairdomhub.org/data_files/1123?version=1
Filename: MODELS-PDB.tar
Format: Tar archive
Size: 2.15 MB
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Views: 1149 Downloads: 44
Created: 29th Apr 2014 at 11:47
Last updated: 10th Jun 2014 at 14:49
Last used: 21st Aug 2017 at 12:07
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Related items
Projects: SysMO-LAB
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH), University of Heidelberg
Comparative Systems Biology: Lactic Acid Bacteria
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=57
Challenge: Comparative analyses, as demonstrated by comparative genomics and bioinformatics, are extremely powerful for (i) transfer of information from (experimentally) well-studied organisms to the other organisms, and (ii) when coupled to functional and phenotypic information, insight in the relative importance of components to the observed differences and simalities. The central principle of this proposal is that important aspects of the functional differences between organisms derive not
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Studies: Comparative modeling and phosphate dependence flux distributions and glu..., Kinetics of L-lactate dehydrogenase from S. pyogenes, E. faecalis and L...., Reconstructing the metabolic pathways of S. pyogenes and E. faecalis fro..., Study of the physiological characterization of three lactic acid bacteri...
The two lactic acid bacteria L. lactis and S. pyogenes were studied with respect to the concentration of intracellular metabolites involved in glycolysis in time upon a glucose pulse. Models that describe this behavior are also constructed
Person responsible: Martijn Bekker
Assays: Global sensitivity analysis, Glucose pulsed L. lactis, Glucose pulsed S. pyogenes, Kinetics of L-lactate dehydrogenase from L. lactis, Model of L. lactis glycolysis, Regulation of the activity of lactate dehydrogenases from four lactic ac...
Despite high similarity in sequence and catalytic properties, the L-lactate dehydrogenases (LDH) in lactic acid bacteria (LAB) display differences in their regulation which may arise from their adaptation to different habitats. We combined experimental and computational approaches to investigate the effects of fructose-1,6-bisphosphate (FBP), phosphate (Pi) and ionic strength (NaCl concentration) on 6 LDHs from 4 LABs studied at pH 6 and pH 7. We find: (1) The extent of activation by FBP (Kact)
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Contributor: Anna Feldman-Salit
Biological problem addressed: Metabolism
Investigation: Investigation of glycolysis and pyruvate branch...
Abstract:
Authors: Anna Feldman-Salit, Silvio Hering, Nadine Veith, Vlad Cojocaru, Antje Sieg, Hans Westerhoff, Bernd Kreikemeyer, Rebecca Wade, Tomas Fiedler, Messiha H.
Date Published: 17th May 2013
Journal: Journal of Biological Chemistry
