scholarly journals Structural basis of terephthalate recognition by solute binding protein TphC

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Trishnamoni Gautom ◽  
Dharmendra Dheeman ◽  
Colin Levy ◽  
Thomas Butterfield ◽  
Guadalupe Alvarez Gonzalez ◽  
...  
Keyword(s):  
Genetic Resource ◽  
Binding Protein ◽  
Structural Basis ◽  
Bacterial Cells ◽  
Ligand Specificity ◽  
Biological Degradation ◽  
Genomic Context ◽  
Context Analysis ◽  
Structural Characterisation ◽  
Genomic Context Analysis

AbstractBiological degradation of Polyethylene terephthalate (PET) plastic and assimilation of the corresponding monomers ethylene glycol and terephthalate (TPA) into central metabolism offers an attractive route for bio-based molecular recycling and bioremediation applications. A key step is the cellular uptake of the non-permeable TPA into bacterial cells which has been shown to be dependent upon the presence of the key tphC gene. However, little is known from a biochemical and structural perspective about the encoded solute binding protein, TphC. Here, we report the biochemical and structural characterisation of TphC in both open and TPA-bound closed conformations. This analysis demonstrates the narrow ligand specificity of TphC towards aromatic para-substituted dicarboxylates, such as TPA and closely related analogues. Further phylogenetic and genomic context analysis of the tph genes reveals homologous operons as a genetic resource for future biotechnological and metabolic engineering efforts towards circular plastic bio-economy solutions.

scholarly journals Structural basis of terephthalate recognition by solute binding protein TphC

2021 ◽  
Author(s):  
Trishna Gautom ◽  
Dharmendra Dheeman ◽  
Colin Levy ◽  
Thomas Butterfield ◽  
Lewis Caiger ◽  
...  
Keyword(s):  
Genetic Resource ◽  
Binding Protein ◽  
Structural Basis ◽  
Bacterial Cells ◽  
Ligand Specificity ◽  
Biological Degradation ◽  
Genomic Context ◽  
Context Analysis ◽  
Structural Characterisation ◽  
Genomic Context Analysis

Abstract Biological degradation of Polyethylene terephthalate (PET) plastic and assimilation of the corresponding monomers ethylene glycol and terephthalate (TPA) into central metabolism offers an attractive route for bio-based molecular recycling and bioremediation applications. A key step is the cellular uptake of the non-permeable TPA into bacterial cells which has been shown to be dependent upon the presence of the key tphC gene. However, little is known from a biochemical and structural perspective about the encoded solute binding protein, TphC. Here, we report the biochemical and structural characterisation of TphC in both open and TPA-bound closed conformations. This analysis demonstrates the narrow ligand specificity of TphC towards aromatic para-substituted dicarboxylates, such as TPA and closely related analogues. Further phylogenetic and genomic context analysis of the tph genes reveals homologous operons as a genetic resource for future biotechnological and metabolic engineering efforts towards circular plastic bio-economy solutions.

scholarly journals Evolutionary and functional relationships revealed by the dha regulon predicted by genomic context analysis

2011 ◽  
Vol 12 (S1) ◽  
Author(s):  
Marinalva Martins-Pinheiro ◽  
Wanessa Cristina Lima ◽  
Cláudio A Oller ◽  
Carlos FM Menck
Keyword(s):  
Genomic Context ◽  
Context Analysis ◽  
Functional Relationships ◽  
Genomic Context Analysis ◽  
Dha Regulon

scholarly journals Genomic Context Analysis ofde Novo STXBP1Mutations Identifies Evidence of Splice Site DNA-Motif Associated Hotspots

2018 ◽  
Vol 8 (4) ◽  
pp. 1115-1118 ◽  
Author(s):  
Mohammed Uddin ◽  
Marc Woodbury-Smith ◽  
Ada J. S. Chan ◽  
Ammar Albanna ◽  
Berge Minassian ◽  
...  
Keyword(s):  
Splice Site ◽  
Genomic Context ◽  
Context Analysis ◽  
Dna Motif ◽  
Genomic Context Analysis

scholarly journals Prediction of enzymatic pathways by integrative pathway mapping

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Sara Calhoun ◽  
Magdalena Korczynska ◽  
Daniel J Wichelecki ◽  
Brian San Francisco ◽  
Suwen Zhao ◽  
...  
Keyword(s):  
Structural Biology ◽  
Metabolic Networks ◽  
Mapping Method ◽  
Computational Method ◽  
Molecular Networks ◽  
Genomic Context ◽  
Context Analysis ◽  
Pathway Mapping ◽  
Genomic Context Analysis ◽  
Enzymatic Pathways

The functions of most proteins are yet to be determined. The function of an enzyme is often defined by its interacting partners, including its substrate and product, and its role in larger metabolic networks. Here, we describe a computational method that predicts the functions of orphan enzymes by organizing them into a linear metabolic pathway. Given candidate enzyme and metabolite pathway members, this aim is achieved by finding those pathways that satisfy structural and network restraints implied by varied input information, including that from virtual screening, chemoinformatics, genomic context analysis, and ligand -binding experiments. We demonstrate this integrative pathway mapping method by predicting the L-gulonate catabolic pathway in Haemophilus influenzae Rd KW20. The prediction was subsequently validated experimentally by enzymology, crystallography, and metabolomics. Integrative pathway mapping by satisfaction of structural and network restraints is extensible to molecular networks in general and thus formally bridges the gap between structural biology and systems biology.

scholarly journals Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes

2004 ◽  
Vol 32 (21) ◽  
pp. 6321-6326 ◽  
Author(s):  
Tobias Doerks ◽  
Christian von Mering ◽  
Peer Bork
Keyword(s):  
Hypothetical Proteins ◽  
Genomic Context ◽  
Context Analysis ◽  
Genomic Context Analysis

scholarly journals The Structural Basis of the Binding of Various Aminopolycarboxylates by the Periplasmic EDTA-Binding Protein EppA from Chelativorans sp. BNC1

2020 ◽  
Vol 21 (11) ◽  
pp. 3940 ◽  
Author(s):  
Kevin M. Lewis ◽  
Chelsie L. Greene ◽  
Steven A. Sattler ◽  
Buhyun Youn ◽  
Luying Xun ◽  
...  
Keyword(s):  
Binding Protein ◽  
Metal Chelate ◽  
Binding Pocket ◽  
Site Directed Mutagenesis ◽  
Structural Basis ◽  
Titration Calorimetry ◽  
Bacterial Cells ◽  
Chelate Complexes ◽  
Quantum Chemical Analysis ◽  
Ligand Selectivity

The widespread use of synthetic aminopolycarboxylates, such as ethylenediaminetetraacetate (EDTA), as chelating agents has led to their contamination in the environment as stable metal–chelate complexes. Microorganisms can transport free EDTA, but not metal–EDTA complexes, into cells for metabolism. An ABC-type transporter for free EDTA uptake in Chelativorans sp. BNC1 was investigated to understand the mechanism of the ligand selectivity. We solved the X-ray crystal structure of the periplasmic EDTA-binding protein (EppA) and analyzed its structure–function relations through isothermal titration calorimetry, site-directed mutagenesis, molecular docking, and quantum chemical analysis. EppA had high affinities for EDTA and other aminopolycarboxylates, which agrees with structural analysis, showing that its binding pocket could accommodate free aminopolycarboxylates. Further, key amino acid residues involved in the binding were identified. Our results suggest that EppA is a general binding protein for the uptake of free aminopolycarboxylates. This finding suggests that bacterial cells import free aminopolycarboxylates, explaining why stable metal–chelate complexes are resistant to degradation, as they are not transported into the cells for degradation.

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