Structural Basis for the ADP-Specificity of a Novel Glucokinase from a Hyperthermophilic Archaeon

Ito, Sohei; Fushinobu, Shinya; Yoshioka, Ichiro; Koga, Shinji; Matsuzawa, Hiroshi; Wakagi, Takayoshi

doi:10.1016/s0969-2126(01)00577-9

Cited by 89 publications

(118 citation statements)

References 31 publications

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“…This fold is similar to the core structure of the ribokinase superfamily (Fig. 2, b and c), which includes ribokinase (22), human adenosine kinase (34), adenosine kinase from Toxoplasma gondii (24), 4-methy-5-␤-hydroxyethylthiazole (THZ) kinase (35), ADP-specificity glucokinase (36), and the recently reported 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate (HMPP) kinase (25). Despite the structural similarity, the amino acid identity between pyridoxal kinase and any of these kinases is low, and only part of the sequence can be aligned.…”

Section: Resultsmentioning

confidence: 71%

Crystal Structure of Brain Pyridoxal Kinase, a Novel Member of the Ribokinase Superfamily

Kwok

Chang

et al. 2002

Journal of Biological Chemistry

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The three-dimensional structures of brain pyridoxal kinase and its complex with the nucleotide ATP have been elucidated in the dimeric form at 2.1 and 2.6 Å, respectively. Results have shown that pyridoxal kinase, as an enzyme obeying random sequential kinetics in catalysis, does not possess a lid shape structure common to all kinases in the ribokinase superfamily. This finding has been shown to be in line with the condition that pyridoxal kinase binds substrates with variable sizes of chemical groups at position 4 of vitamin B 6 and its derivatives. In addition, the enzyme contains a 12-residue peptide loop in the active site for the prevention of premature hydrolysis of ATP. Conserved amino acid residues Asp 118 and Tyr 127 in the peptide loop could be moved to a position covering the nucleotide after its binding so that its chance to hydrolyze in the aqueous environment of the active site was reduced. With respect to the evolutionary trend of kinase enzymes, the existence of this loop in pyridoxal kinase could be classified as an independent category in the ribokinase superfamily according to the structural feature found and mechanism followed in catalysis.

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Section: Resultsmentioning

confidence: 71%

Crystal Structure of Brain Pyridoxal Kinase, a Novel Member of the Ribokinase Superfamily

Kwok

Chang

et al. 2002

Journal of Biological Chemistry

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“…5) (19 -21). It was initially reported that the TlGK structure was the most open conformation because they were able to successfully soak ADP out of the crystal, which indicates the absence of a large conformational change (19). The PhGK structure clearly presented a more open conformation, which led to the suggestion that TlGK had been trapped in the ADP-bound conformation following the removal of the ADP from the crystal (21).…”

Section: Resultsmentioning

confidence: 99%

“…It could be that the ␤-phosphate of ADP is required to fully induce this conformational change. The amine nitrogen of Arg-205 from TlGK is 3.8 Å away from the ␤-phosphate of ADP and may form important interactions that help to stabilize a more closed conformation (19). One other possibility is that for PhPFK both co-factor and substrate are required for the conformational change observed as seen in other structures.…”

Section: Resultsmentioning

confidence: 99%

“…Despite low sequence identity between ADP-GKs and other kinases (e.g. PhGK shares 11 and 12% identity with E. coli ribokinase and human adenosine kinase, respectively) the fold is similar to that of ribokinases (19). As a result, ADP-GKs have been classified as members of the ribokinase superfamily (19).…”

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confidence: 99%

“…Upon glucose binding, the protein undergoes a conformational change whereby the large and small domains close in creating the active-site pocket (20). Interestingly, the unique ADP binding pocket of ADP-GKs recognizes the ␣-and ␤-phosphate of the ADP in an almost identical manner to how the ␤-and ␥-phosphate of ATP are recognized in ATP-dependent kinases of the ribokinase superfamily (19).…”

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confidence: 99%

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ADP-dependent 6-Phosphofructokinase from Pyrococcus horikoshii OT3

Currie

Merino

Skarina

et al. 2009

Journal of Biological Chemistry

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Some hyperthermophilic archaea use a modified glycolytic pathway that employs an ADP-dependent glucokinase (ADP-GK) and an ADP-dependent phosphofructokinase (ADP-PFK) or, in the case of Methanococcus jannaschii, a bifunctional ADPdependent glucophosphofructokinase (ADP-GK/PFK). The crystal structures of three ADP-GKs have been determined. However, there is no structural information available for ADPPFKs or the ADP-GK/PFK. Here, we present the first crystal structure of an ADP-PFK from Pyrococcus horikoshii OT3 (PhPFK) in both apo-and AMP-bound forms determined to 2.0-Å and 1.9-Å resolution, respectively, along with biochemical characterization of the enzyme. The overall structure of PhPFK maintains a similar large and small ␣/␤ domain structure seen in the ADP-GK structures. A large conformational change accompanies binding of phosphoryl donor, acceptor, or both, in all members of the ribokinase superfamily characterized thus far, which is believed to be critical to enzyme function. Surprisingly, no such conformational change was observed in the AMPbound PhPFK structure compared with the apo structure. Through comprehensive site-directed mutagenesis of the substrate binding pocket we identified residues that were critical for both substrate recognition and the phosphotransfer reaction. The catalytic residues and many of the substrate binding residues are conserved between PhPFK and ADP-GKs; however, four key residues differ in the sugar-binding pocket, which we have shown determine the sugar-binding specificity. Using these results we were able to engineer a mutant PhPFK that mimics the ADP-GK/PFK and is able to phosphorylate both fructose 6-phosphate and glucose.

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The ADP‐dependent sugar kinase family: Kinetic and evolutionary aspects

Guixé

Merino

2009

IUBMB Life

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SummarySome archaea of the Euryarchaeota present a unique version of the Embden-Meyerhof pathway where glucose and fructose-6-phosphate are phoshporylated using ADP instead of ATP as the phosphoryl donor. These are the only ADP-dependent kinases known to date. Although initially they were believed to represent a new protein family, they can be classified as members of the ribokinase superfamily, which also include several ATP-dependent kinases. As they were first identified in members of the thermococcales it was proposed that the presence of these ADP-dependent kinases is an adaptation to high temperatures. Later, homologs of these enzymes were identified in the genomes of mesophilic and thermophilic methanogenic archaea and even in the genomes of higher eukaryotes, suggesting that the presence of these proteins is not related to the hyperthermophilic life. The ADP-dependent kinases are very restrictive to their ligands being unable to use triphosphorylated nucleotides such as ATP. However, it has been shown that they can bind ATP by competition kinetic experiments. The hyperthermophilic methanogenic archaeon Methanocaldococcus jannaschii has a homolog of these genes, which can phosphorylate glucose and fructose-6-phosphate. For this reason, it was proposed as an ancestral form for the family. However, recent studies have shown that the ancestral activity in the group is glucokinase, and a combination of gene duplication and lateral gene transfer could have originated the two paralogs in this member of the Euryarchaeota. Interestingly, based on structural comparisons made within the superfamily it has been suggested that the ADP-dependent kinases are the newest in the group. In several members of the superfamily, the presence of divalent metal cations has been shown to be crucial for catalysis, so its role in the ADP-dependent family was investigated through molecular dynamics. The simulation shows that, in fact, the metal coordinates the catalytic ensemble and interacts with crucial residues for catalysis. Keywords ADP-dependent kinase family; ribokinase superfamily; modified Embden-Meyerhof pathway; glucokinase; phosphofructokinase.Abbreviations ADP-GK, ADP-dependent glucokinase; ADP-PFK, ADP-dependent phosphofructokinase; ThzK, 4-Methyl-5-b-hydroxyethylthiazole kinase; HmppK, 4-amino-5-hydroxymethyl-2-methylpyrimidine kinase.

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Structural Basis for the ADP-Specificity of a Novel Glucokinase from a Hyperthermophilic Archaeon

Cited by 89 publications

References 31 publications

Crystal Structure of Brain Pyridoxal Kinase, a Novel Member of the Ribokinase Superfamily

Crystal Structure of Brain Pyridoxal Kinase, a Novel Member of the Ribokinase Superfamily

ADP-dependent 6-Phosphofructokinase from Pyrococcus horikoshii OT3

The ADP‐dependent sugar kinase family: Kinetic and evolutionary aspects

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