Open–close structural change upon ligand binding and two magnesium ions required for the catalysis of N-acetylhexosamine 1-kinase

Sato, Mayo; Arakawa, T.; Nam, Young‐Woo; Nishimoto, Mamoru; Kitaoka, Motomitsu; Fushinobu, Shinya

doi:10.1016/j.bbapap.2015.01.011

Cited by 15 publications

(21 citation statements)

References 29 publications

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“…Note that the first report of NahK structure wrongly designates its name as ‘ N -acetylhexosamine 1-phosphate kinase’. A large open-close conformational change in NahK was observed, and two Mg 2+ in the ATP-binding site facilitate the catalysis ( Figure 2B ) [ 39 , 40 ]. GalE catalyses the interconversion of gluco - and galacto -hexoses (C4 epimerization) linked to UDP.…”

Section: Import and Degradation Of Host-derived Glycansmentioning

confidence: 99%

Structure and evolution of the bifidobacterial carbohydrate metabolism proteins and enzymes

Fushinobu

Hachem

2021

Biochemical Society Transactions

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Bifidobacteria have attracted significant attention because they provide health-promoting effects in the human gut. In this review, we present a current overview of the three-dimensional structures of bifidobacterial proteins involved in carbohydrate uptake, degradation, and metabolism. As predominant early colonizers of the infant's gut, distinct bifidobacterial species are equipped with a panel of transporters and enzymes specific for human milk oligosaccharides (HMOs). Interestingly, Bifidobacterium bifidum and Bifidobacterium longum possess lacto-N-biosidases with unrelated structural folds to release the disaccharide lacto-N-biose from HMOs, suggesting the convergent evolution of this activity from different ancestral proteins. The crystal structures of enzymes that confer the degradation of glycans from the mucin glycoprotein layer provide a structural basis for the utilization of this sustainable nutrient in the gastrointestinal tract. The utilization of several plant dietary oligosaccharides has been studied in detail, and the prime importance of oligosaccharide-specific ATP-binding cassette (ABC) transporters in glycan utilisations by bifidobacteria has been revealed. The structural elements underpinning the high selectivity and roles of ABC transporter binding proteins in establishing competitive growth on preferred oligosaccharides are discussed. Distinct ABC transporters are conserved across several bifidobacterial species, e.g. those targeting arabinoxylooligosaccharide and α-1,6-galactosides/glucosides. Less prevalent transporters, e.g. targeting β-mannooligosaccharides, may contribute to the metabolic specialisation within Bifidobacterium. Some bifidobacterial species have established symbiotic relationships with humans. Structural studies of carbohydrate-utilizing systems in Bifidobacterium have revealed the interesting history of molecular coevolution with the host, as highlighted by the early selection of bifidobacteria by mucin and breast milk glycans.

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Section: Import and Degradation Of Host-derived Glycansmentioning

confidence: 99%

Structure and evolution of the bifidobacterial carbohydrate metabolism proteins and enzymes

Fushinobu

Hachem

2021

Biochemical Society Transactions

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“…Fig. 4(a) shows the typical binding mode of magnesium ions by the phosphate groups of ADP in complex with N-acetylhexosamine 1-kinase (Sato et al, 2015). In this high-resolution structure (1.8 Å ) magnesium ions are bound to their interaction partners by six coordination bonds, which must be always arranged in an octahedral molecular geometry.…”

Section: Figurementioning

confidence: 99%

No magnesium is needed for binding of the stimulator of interferon genes to cyclic dinucleotides

Smola

Birkuš

Bouřa

2019

Acta Crystallogr F Struct Biol Commun

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Stimulator of interferon genes (STING) binds cyclic dinucleotides (CDNs), which induce a large conformational change of the protein. The structural basis of activation of STING by CDNs is rather well understood. Unliganded STING forms an open dimer that undergoes a large conformational change (∼10 Å) to a closed conformation upon the binding of a CDN molecule. This event activates downstream effectors of STING and subsequently leads to activation of the type 1 interferon response. However, a previously solved structure of STING with 3′,3′‐c‐di‐GMP shows Mg atoms mediating the interaction of STING with this CDN. Here, it is shown that no Mg atoms are needed for this interaction; in fact, magnesium can in some cases obstruct the binding of a CDN to STING.

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“…Phosphoryl transfer. In general, enzymes catalyzing phosphoryl transfer reactions also require two Mg 2ϩ , as demonstrated from studies of Pyrococcus furiosus UMP kinase (PDB code 2bmu) (197), Staphylococcus aureus tagatose 6-phosphate kinase (PDB code 2jg1) (198), Bifidobacterium longum N-acetylhexosamine kinase (PDB code 4wh3) (199), mammalian cyclin-dependent kinase 2 (PDB code 3qhw) (200), or cyclic AMP (cAMP)-dependent protein kinase A (PDB codes 1l3r and 4hpu) (201,202). We shall use protein kinase A for a more detailed description.…”

Section: Substitution Reactions At ␣- ␤- or ␥-Phosphatesmentioning

confidence: 99%

Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance

Hove‐Jensen

Andersen

Kilstrup

et al. 2017

Microbiol Mol Biol Rev

157

187

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SUMMARY Phosphoribosyl diphosphate (PRPP) is an important intermediate in cellular metabolism. PRPP is synthesized by PRPP synthase, as follows: ribose 5-phosphate + ATP → PRPP + AMP. PRPP is ubiquitously found in living organisms and is used in substitution reactions with the formation of glycosidic bonds. PRPP is utilized in the biosynthesis of purine and pyrimidine nucleotides, the amino acids histidine and tryptophan, the cofactors NAD and tetrahydromethanopterin, arabinosyl monophosphodecaprenol, and certain aminoglycoside antibiotics. The participation of PRPP in each of these metabolic pathways is reviewed. Central to the metabolism of PRPP is PRPP synthase, which has been studied from all kingdoms of life by classical mechanistic procedures. The results of these analyses are unified with recent progress in molecular enzymology and the elucidation of the three-dimensional structures of PRPP synthases from eubacteria, archaea, and humans. The structures and mechanisms of catalysis of the five diphosphoryltransferases are compared, as are those of selected enzymes of diphosphoryl transfer, phosphoryl transfer, and nucleotidyl transfer reactions. PRPP is used as a substrate by a large number phosphoribosyltransferases. The protein structures and reaction mechanisms of these phosphoribosyltransferases vary and demonstrate the versatility of PRPP as an intermediate in cellular physiology. PRPP synthases appear to have originated from a phosphoribosyltransferase during evolution, as demonstrated by phylogenetic analysis. PRPP, furthermore, is an effector molecule of purine and pyrimidine nucleotide biosynthesis, either by binding to PurR or PyrR regulatory proteins or as an allosteric activator of carbamoylphosphate synthetase. Genetic analyses have disclosed a number of mutants altered in the PRPP synthase-specifying genes in humans as well as bacterial species.

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Open–close structural change upon ligand binding and two magnesium ions required for the catalysis of N-acetylhexosamine 1-kinase

Cited by 15 publications

References 29 publications

Structure and evolution of the bifidobacterial carbohydrate metabolism proteins and enzymes

Structure and evolution of the bifidobacterial carbohydrate metabolism proteins and enzymes

No magnesium is needed for binding of the stimulator of interferon genes to cyclic dinucleotides

Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance

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