Catalytic and regulatory roles of divalent metal cations on the phosphoryl-transfer mechanism of ADP-dependent sugar kinases from hyperthermophilic archaea

Merino, Felipe; Rivas‐Pardo, Jaime Andrés; Caniuguir, A.; García, Inmaculada Moreno; Guixé, Victoria

doi:10.1016/j.biochi.2011.08.021

Cited by 12 publications

(24 citation statements)

References 37 publications

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“…The enzyme was purified as described by Merino et al , [32]. Briefly, the cells from 1L of LB broth were harvested by centrifugation and disrupted by sonication.…”

Section: Methodsmentioning

confidence: 99%

Crystal Structure, SAXS and Kinetic Mechanism of Hyperthermophilic ADP-Dependent Glucokinase from Thermococcus litoralis Reveal a Conserved Mechanism for Catalysis

et al. 2013

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ADP-dependent glucokinases represent a unique family of kinases that belong to the ribokinase superfamily, being present mainly in hyperthermophilic archaea. For these enzymes there is no agreement about the magnitude of the structural transitions associated with ligand binding and whether they are meaningful to the function of the enzyme. We used the ADP-dependent glucokinase from Termococcus litoralis as a model to investigate the conformational changes observed in X-ray crystallographic structures upon substrate binding and to compare them with those determined in solution in order to understand their interplay with the glucokinase function. Initial velocity studies indicate that catalysis follows a sequential ordered mechanism that correlates with the structural transitions experienced by the enzyme in solution and in the crystal state. The combined data allowed us to resolve the open-closed conformational transition that accounts for the complete reaction cycle and to identify the corresponding clusters of aminoacids residues responsible for it. These results provide molecular bases for a general mechanism conserved across the ADP-dependent kinase family.

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“…The enzyme was purified as described by Merino et al , [32]. Briefly, the cells from 1L of LB broth were harvested by centrifugation and disrupted by sonication.…”

Section: Methodsmentioning

confidence: 99%

Crystal Structure, SAXS and Kinetic Mechanism of Hyperthermophilic ADP-Dependent Glucokinase from Thermococcus litoralis Reveal a Conserved Mechanism for Catalysis

et al. 2013

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“…3). Asparagine and glutamate of the NXXE motif are proposed to be involved in bivalent metal cation and nucleotide binding (57,62). ADP-GLKs depend strictly on bivalent metal ions, which coordinate proper nucleotide binding and positioning of the phosphate groups for the phosphoryl transfer reaction (51,53,54,57,62).…”

Section: Glucose Phosphorylationmentioning

confidence: 99%

“…Recently, a third motif (HXE), with a highly conserved glutamate involved in metal ion coordination, has been identified. Furthermore, binding of a second metal ion to another conserved sequence motif in ADP-dependent sugar kinases with regulatory implications has been proposed (62). However, all of the ADPdependent sugar kinases, including those from Archaea reported so far, did not show any regulatory properties like cooperativity or allosteric control, thus differing from eukaryotic hexokinases, which represent one of the sites of allosteric control in the classical EMP pathway (56).…”

Section: Glucose Phosphorylationmentioning

confidence: 99%

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

280

294

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SUMMARY The metabolism of Archaea , the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya . However, this metabolic complexity in Archaea is accompanied by the absence of many “classical” pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of “new,” unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea . In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya . Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.

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“…The R228A ADPGK is predicted to be unable to stabilize the terminal phosphate sufficiently during the reaction, whereas the substrate binding is affected to a lesser extent. A metal ion complexed with ADP is essential for ADPGK activity (32), although to date no definitive site for cation binding has been confirmed for any of the ADPGK crystal structures, as is the case for the mADPGK structures reported here. An exact role for the Mg 2ϩ has not been elucidated, although for ribokinases, it has been hypothesized to stabilize transition state formation by increasing the electrophilicity of the phosphate for transfer (33).…”

Section: Discussionmentioning

confidence: 83%

The Structural and Functional Characterization of Mammalian ADP-dependent Glucokinase

Richter

Goroncy

Ronimus

et al. 2016

Journal of Biological Chemistry

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The enzyme-catalyzed phosphorylation of glucose to glucose-6-phosphate is a reaction central to the metabolism of all life. ADP-dependent glucokinase (ADPGK) catalyzes glucose-6-phosphate production, utilizing ADP as a phosphoryl donor in contrast to the more well characterized ATP-requiring hexokinases. ADPGK is found in Archaea and metazoa; in Archaea, ADPGK participates in a glycolytic role, but a function in most eukaryotic cell types remains unknown. We have determined structures of the eukaryotic ADPGK revealing a ribokinase-like tertiary fold similar to archaeal orthologues but with significant differences in some secondary structural elements. Both the unliganded and the AMP-bound ADPGK structures are in the "open" conformation. The structures reveal the presence of a disulfide bond between conserved cysteines that is positioned at the nucleotide-binding loop of eukaryotic ADPGK. The AMPbound ADPGK structure defines the nucleotide-binding site with one of the disulfide bond cysteines coordinating the AMP with its main chain atoms, a nucleotide-binding motif that appears unique to eukaryotic ADPGKs. Key amino acids at the active site are structurally conserved between mammalian and archaeal ADPGK, and site-directed mutagenesis has confirmed residues essential for enzymatic activity. ADPGK is substrate inhibited by high glucose concentration and shows high specificity for glucose, with no activity for other sugars, as determined by NMR spectroscopy, including 2-deoxyglucose, the glucose analogue used for tumor detection by positron emission tomography.Glucose metabolism is central to the biochemistry of all living systems with the enzymatic phosphorylation of glucose playing a key role in cellular energy metabolism by ensuring that this energy-rich substrate is available to the cell. A relatively recently discovered ADP-dependent glucokinase (ADPGK) 3 (EC 2.7.1.147) catalyzes the phosphorylation of D-glucose to glucose-6-phosphate using MgADP as phosphoryl donor in contrast to the more typical ATP-utilizing hexokinases and glucokinases. ADPGK was first identified in Archaea, being involved in a modified Embden-Meyerhof glycolytic pathway (1), in which Archaea can also use an ADP-dependent phosphofructokinase (ADPPFK; EC 2.7.1.146). Bioinformatic analysis led to the identification of ADPGK in metazoa and the subsequent cloning and initial characterization of mammalian ADPGKs (2, 3). Mammalian ADPGKs show modest sequence similarity to archaeal orthologues (ϳ20% amino acid identity). ADPGK is highly expressed in a wide variety of both normal and tumor mammalian tissues (3) and has been found to be localized to the endoplasmic reticulum in T cells (4) consistent with the sequence-based annotation of an N-terminal signal peptide. Furthermore, ADPGK has been identified as a cholesterol binding protein in a proteomics screen (5). Despite the role of archaeal ADPGK in glycolysis, overexpression of ADPGK in H460 and HC116 human tumor cells showed no cell proliferative or glycolytic effects (3). ADPGK knock-out in t...

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Catalytic and regulatory roles of divalent metal cations on the phosphoryl-transfer mechanism of ADP-dependent sugar kinases from hyperthermophilic archaea

Cited by 12 publications

References 37 publications

Crystal Structure, SAXS and Kinetic Mechanism of Hyperthermophilic ADP-Dependent Glucokinase from Thermococcus litoralis Reveal a Conserved Mechanism for Catalysis

Crystal Structure, SAXS and Kinetic Mechanism of Hyperthermophilic ADP-Dependent Glucokinase from Thermococcus litoralis Reveal a Conserved Mechanism for Catalysis

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

The Structural and Functional Characterization of Mammalian ADP-dependent Glucokinase

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