Structural basis for multiple ligand specificity of the periplasmic lysine-, arginine-, ornithine-binding protein

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.

Download Full-text

Crystal Structure of a Glutamate/Aspartate Binding Protein Complexed with a Glutamate Molecule: Structural Basis of Ligand Specificity at Atomic Resolution

Journal of Molecular Biology ◽

10.1016/j.jmb.2008.06.091 ◽

2008 ◽

Vol 382 (1) ◽

pp. 99-111 ◽

Cited By ~ 19

Author(s):

Yonglin Hu ◽

Cheng-Peng Fan ◽

Guangsen Fu ◽

Deyu Zhu ◽

Qi Jin ◽

...

Keyword(s):

Crystal Structure ◽

Binding Protein ◽

Atomic Resolution ◽

Structural Basis ◽

Ligand Specificity

Download Full-text

Structural basis of terephthalate recognition by solute binding protein TphC

10.21203/rs.3.rs-358367/v1 ◽

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.

Download Full-text

Structural Basis of the Broad Specificity of a General Odorant-Binding Protein from Honeybee

Biochemistry ◽

10.1021/bi802300k ◽

2009 ◽

Vol 48 (11) ◽

pp. 2431-2441 ◽

Cited By ~ 39

Author(s):

Ewen Lescop ◽

Loïc Briand ◽

Jean-Claude Pernollet ◽

Eric Guittet

Keyword(s):

Binding Protein ◽

Odorant Binding Protein ◽

Structural Basis ◽

Odorant Binding ◽

Broad Specificity

Download Full-text

Structural characterization of amorphous calcium carbonate-binding protein: an insight into the mechanism of amorphous calcium carbonate formation

Biochemical Journal ◽

10.1042/bj20130285 ◽

2013 ◽

Vol 453 (2) ◽

pp. 179-186 ◽

Cited By ~ 14

Author(s):

Jingtan Su ◽

Xiao Liang ◽

Qiang Zhou ◽

Guiyou Zhang ◽

Hongzhong Wang ◽

...

Keyword(s):

Calcium Carbonate ◽

Binding Sites ◽

Binding Protein ◽

Homology Modelling ◽

Size Exclusion ◽

Structural Basis ◽

Amorphous Calcium Carbonate ◽

Carbonate Formation

ACC (amorphous calcium carbonate) plays an important role in biomineralization process for its function as a precursor for calcium carbonate biominerals. However, it is unclear how biomacromolecules regulate the formation of ACC precursor in vivo. In the present study, we used biochemical experiments coupled with bioinformatics approaches to explore the mechanisms of ACC formation controlled by ACCBP (ACC-binding protein). Size-exclusion chromatography, chemical cross-linking experiments and negative staining electron microscopy reveal that ACCBP is a decamer composed of two adjacent pentamers. Sequence analyses and fluorescence quenching results indicate that ACCBP contains two Ca2+-binding sites. The results of in vitro crystallization experiments suggest that one Ca2+-binding site is critical for ACC formation and the other site affects the ACC induction efficiency. Homology modelling demonstrates that the Ca2+-binding sites of pentameric ACCBP are arranged in a 5-fold symmetry, which is the structural basis for ACC formation. To the best of our knowledge, this is the first report on the structural basis for protein-induced ACC formation and it will significantly improve our understanding of the amorphous precursor pathway.

Download Full-text

Structural basis of nucleic acid binding byNicotiana tabacumglycine-rich RNA-binding protein: implications for its RNA chaperone function

Nucleic Acids Research ◽

10.1093/nar/gku468 ◽

2014 ◽

Vol 42 (13) ◽

pp. 8705-8718 ◽

Cited By ~ 12

Author(s):

Fariha Khan ◽

Mark A. Daniëls ◽

Gert E. Folkers ◽

Rolf Boelens ◽

S. M. Saqlan Naqvi ◽

...

Keyword(s):

Nucleic Acid ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Structural Basis ◽

Nucleic Acid Binding ◽

Rna Chaperone ◽

Chaperone Function

Download Full-text

Structural basis of the zinc-induced cytoplasmic aggregation of the RNA-binding protein SFPQ

Nucleic Acids Research ◽

10.1093/nar/gkaa076 ◽

2020 ◽

Vol 48 (6) ◽

pp. 3356-3365 ◽

Cited By ~ 4

Author(s):

Jie Huang ◽

Mitchell Ringuet ◽

Andrew E Whitten ◽

Sofia Caria ◽

Yee Wa Lim ◽

...

Keyword(s):

Crystal Structure ◽

Cortical Neurons ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Zinc Binding ◽

Structural Basis ◽

Rna Biogenesis ◽

Cytoplasmic Accumulation ◽

Nucleocytoplasmic Distribution

Abstract SFPQ is a ubiquitous nuclear RNA-binding protein implicated in many aspects of RNA biogenesis. Importantly, nuclear depletion and cytoplasmic accumulation of SFPQ has been linked to neuropathological conditions such as Alzheimer's disease (AD) and amyotrophic lateral sclerosis (ALS). Here, we describe a molecular mechanism by which SFPQ is mislocalized to the cytoplasm. We report an unexpected discovery of the infinite polymerization of SFPQ that is induced by zinc binding to the protein. The crystal structure of human SFPQ in complex with zinc at 1.94 Å resolution reveals intermolecular interactions between SFPQ molecules that are mediated by zinc. As anticipated from the crystal structure, the application of zinc to primary cortical neurons induced the cytoplasmic accumulation and aggregation of SFPQ. Mutagenesis of the three zinc-coordinating histidine residues resulted in a significant reduction in the zinc-binding affinity of SFPQ in solution and the zinc-induced cytoplasmic aggregation of SFPQ in cultured neurons. Taken together, we propose that dysregulation of zinc availability and/or localization in neuronal cells may represent a mechanism for the imbalance in the nucleocytoplasmic distribution of SFPQ, which is an emerging hallmark of neurodegenerative diseases including AD and ALS.

Download Full-text