Carbohydrate Kinases: A Conserved Mechanism Across Differing Folds

Roy, Sumita; Vega, Mirella Vivoli; Harmer, Nicholas J.

doi:10.3390/catal9010029

Cited by 28 publications

(32 citation statements)

References 129 publications

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“…GK is classified as a member of the sugar kinase family, also known as FGGY kinases, which in turn belongs to the nucleotide binding-sugar kinase/heat shock protein 70/actin superfamily. Proteins belonging to this superfamily are known to undergo large conformational changes upon substrate binding [ 8 , 9 ].…”

Section: Introductionmentioning

confidence: 99%

Structural Characterization of Glycerol Kinase from the Thermophilic Fungus Chaetomium thermophilum

Wilk

Magiera‐Mularz

Wator

et al. 2020

IJMS

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Glycerol is an organic compound that can be utilized as an alternative source of carbon by various organisms. One of the ways to assimilate glycerol by the cell is the phosphorylative catabolic pathway in which its activation is catalyzed by glycerol kinase (GK) and glycerol-3-phosphate (G3P) is formed. To date, several GK crystal structures from bacteria, archaea, and unicellular eukaryotic parasites have been solved. Herein, we present a series of crystal structures of GK from Chaetomium thermophilum (CtGK) in apo and glycerol-bound forms. In addition, we show the feasibility of an ADP-dependent glucokinase (ADPGK)-coupled enzymatic assay to measure the CtGK activity. New structures described in our work provide structural insights into the GK catalyzed reaction in the filamentous fungus and set the foundation for understanding the glycerol metabolism in eukaryotes.

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Section: Introductionmentioning

confidence: 99%

Structural Characterization of Glycerol Kinase from the Thermophilic Fungus Chaetomium thermophilum

Wilk

Magiera‐Mularz

Wator

et al. 2020

IJMS

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“…E. coli's enzymes xylulokinase is active on xylulose and ribulose (Di Luccio et al, 2007) and fuculokinase is active on fuculose and ribulose (LeBlanc and Mortlock, 1971). One explanation for their promiscuity is that carbohydrate kinases are ancient enzymes, which needed to evolve into niches of present carbon sources (Roy et al, 2019). A good example for enzyme promiscuity is the fast evolution for utilization of new substrates shown for E. coli (Guzman et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Evolving a new efficient mode of fructose utilization for improved bioproduction inCorynebacterium glutamicum

Krahn

Bonder

Torregrosa

et al. 2021

Preprint

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Fructose utilization in Corynebacterium glutamicum starts with its uptake and concomitant phosphorylation via the phosphotransferase system (PTS) to yield intracellular fructose 1-phosphate, which enters glycolysis upon ATP dependent phosphorylation to fructose 1,6-bisphosphate by 1-phosphofructokinase. This is known to result in a significantly reduced oxidative pentose phosphate pathway (oxPPP) flux on fructose (~10 %) compared to glucose (~60 %). Consequently, the biosynthesis of NADPH demanding products, e.g. L-lysine, by C. glutamicum is largely decreased, when fructose is the only carbon source. Previous works reported that fructose is partially utilized via the glucose specific PTS presumably generating fructose 6-phosphate. This closer proximity to the entry point of the oxPPP might increase oxPPP flux and consequently NADPH availability. Here, we generated deletion strains either lacking in the fructose-specific PTS or 1-phosphofructokinase activity. We used these strains in short-term evolution experiments on fructose minimal medium and isolated mutant strains, which regained the ability of fast growth on fructose as a sole carbon source. In these fructose mutants, the deletion of the glucose specific PTS, as well as the 6-phosphofructokinase gene, abolished growth, unequivocally showing fructose phosphorylation via glucose specific PTS to fructose 6-phosphate. Gene sequencing revealed three independent amino acid substitutions in PtsG (M260V, M260T, P318S). These three PtsG variants mediated faster fructose uptake and utilization compared to native PtsG. In-depth analysis of the effects of fructose utilization via these PtsG variants revealed significantly increased biomass formation, reduced side-product accumulation, and increased L-lysine production by 50 %.

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“…This may avoid premature hydrolysis of the γ-phosphate of ATP, as reported in ribokinases. 23,[25][26] Given the close functional relationship between of SF kinase (YihV) and PfkB and TPK, sequence-and structure-based analysis of their binding sites was undertaken. Two conserved motifs have been described in these phosphosugar kinases, the TR and GXGDXX motifs, responsible for substrate binding and catalysis, respectively.…”

Section: Sf Kinase Is Allosterically Regulated By Central Metabolitesmentioning

confidence: 99%

The Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis

Sharma¹,

Abayakoon²,

Epa³

et al. 2021

Preprint

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The sulfosugar sulfoquinovose (SQ) is produced by essentially all photosynthetic organisms on earth and is metabolized bacteria through the process of sulfoglycolysis. The sulfoglycolytic Embden-Meyerhof-Parnas pathway metabolises SQ to produce dihydroxyacetone phosphate and sulfolactaldehyde and is analogous to the classical Embden-Meyerhof-Parnas glycolysis pathway for the metabolism of glucose-6-phosphate, though the former only provides one C3 fragment to central metabolism, with excretion of the other C3 fragment as dihydroxypropanesulfonate. Here, we report a comprehensive structural and biochemical analysis of the three core steps of sulfoglycolysis catalyzed by SQ isomerase, sulfofructose (SF) kinase and sulfofructose-1-phosphate aldolase. Our data shows that despite the superficial similarity of this pathway to glycolysis, the sulfoglycolytic enzymes are specific for SQ metabolites and are not catalytically active on related metabolites from glycolytic pathways. This observation is rationalized by 3D structures of each of these enzymes, which reveal the presence of conserved sulfonate-binding pockets. We show that SQ isomerase acts preferentially on the b-anomer of SQ and reversibly produces both SF and sulforhamnose (SR), a previously unknown sugar that acts as a transcriptional regulator for the transcriptional repressor CsqR that regulates SQ-utilisation. We also demonstrate that SF kinase is a key regulatory enzyme for the pathway that experiences complex allosteric modulation by the metabolites AMP, ADP, ATP, F6P, FBP, PEP, and citrate. This body of work provides fresh insights into the mechanism, specificity and regulation of sulfoglycolysis and has important implications for understanding how this biochemistry interfaces with central metabolism in prokaryotes to process this major repository of biogeochemical sulfur.

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Carbohydrate Kinases: A Conserved Mechanism Across Differing Folds

Cited by 28 publications

References 129 publications

Structural Characterization of Glycerol Kinase from the Thermophilic Fungus Chaetomium thermophilum

Structural Characterization of Glycerol Kinase from the Thermophilic Fungus Chaetomium thermophilum

Evolving a new efficient mode of fructose utilization for improved bioproduction inCorynebacterium glutamicum

The Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis

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