Crystal structure of UDP-galactose 4-epimerase from the hyperthermophilic archaeon Pyrobaculum calidifontis

Sakuraba, Haruhiko; Kawai, Tadao; Yoneda, Kazunari; Ohshima, Toshihisa

doi:10.1016/j.abb.2011.05.013

Cited by 28 publications

(25 citation statements)

References 29 publications

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“…[24–26] are important in the viability of these pathogens, and GALE is also essential for survival of the “model” multicellular eukaryote Drosophila melanogaster [27]. The crystal structures of GALE from a variety of different species interacting with various substrates and substrate analogues are also known providing insight into how the enzyme functions [15;16;28–31]. The human GALE structure has been an invaluable tool in understanding how mutations can affect the enzyme and the structure of the variant associated with the most common severe phenotype, p.V94M, has been solved [32].…”

Section: Introductionmentioning

confidence: 99%

Altered cofactor binding affects stability and activity of human UDP-galactose 4′-epimerase: Implications for type III galactosemia

McCorvie

Liu

Frazer

et al. 2012

Biochimica et Biophysica Acta (BBA) - Molecular Basis of Diseas

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Deficiency of UDP-galactose 4′-epimerase is implicated in type III galactosemia. Two variants, p.K161N-hGALE and p.D175N-hGALE, have been previously found in combination with other alleles in patients with a mild form of the disease. Both variants were studied in vivo and in vitro and showed different levels of impairment. p.K161N-hGALE was severely impaired with substantially reduced enzymatic activity, increased thermal stability, reduced cofactor binding and inability to rescue the galactose-sensitivity of gal10-null yeast. Interestingly p.K161N-hGALE showed less impairment of activity with UDP-N-acetylgalactosamine in comparison to UDP-galactose. Differential scanning fluorimetry revealed that p.K161N-hGALE was more stable than the wild-type protein and only changed stability in the presence of UDP-N-acetylglucosamine and NAD+. p.D175N-hGALE essentially rescued the galactose-sensitivity of gal10-null yeast, was less stable than the wild-type protein but showed increased stability in the presence of substrates and cofactor. We postulate that p.K161N-hGALE causes its effects by abolishing an important interaction between the protein and the cofactor, whereas p.D175N-hGALE is predicted to remove a stabilizing salt bridge between the ends of two α-helices that contain residues that interact with NAD+. These results suggest that the cofactor binding is dynamic and that its loss results in significant structural changes that may be important in disease causation.

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Section: Introductionmentioning

confidence: 99%

Altered cofactor binding affects stability and activity of human UDP-galactose 4′-epimerase: Implications for type III galactosemia

McCorvie

Liu

Frazer

et al. 2012

Biochimica et Biophysica Acta (BBA) - Molecular Basis of Diseas

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“…Several spectrometric methods, such as hydrogen-deuterium exchange and fluorescence methods (36), are helpful in understanding structural changes at various time scales (from s to s) that are difficult to analyze by MD simulation. As for other members of the extended SDR superfamily, both crystallography and computer simulation studies (37)(38)(39) have suggested that GalE undergoes structural changes during its reaction. Specifically, x-ray crystal structures indicated that the catalytic domain of GalE is flexible, just as that of SDR-like L-ThrDH is, when substrate is not bound to the active site (39).…”

Section: Molecular Dynamics Simulation Of Cnthrdh (Holo With Nadmentioning

confidence: 99%

“…As for other members of the extended SDR superfamily, both crystallography and computer simulation studies (37)(38)(39) have suggested that GalE undergoes structural changes during its reaction. Specifically, x-ray crystal structures indicated that the catalytic domain of GalE is flexible, just as that of SDR-like L-ThrDH is, when substrate is not bound to the active site (39). Furthermore, using MD simulation, Friedman et al (38) showed that induced fit and structural changes of the catalytic domain are likely to play a role in the binding of substrates to the active site of GalE.…”

Section: Molecular Dynamics Simulation Of Cnthrdh (Holo With Nadmentioning

confidence: 99%

Binding of NAD+ and l-Threonine Induces Stepwise Structural and Flexibility Changes in Cupriavidus necator l-Threonine Dehydrogenase

Nakano

Okazaki

Tokiwa

et al. 2014

Journal of Biological Chemistry

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“…BLAST searches reveal numerous proteins, described as UDP-glucose-4-epimerases, in both Archaea and Bacteria that have very high sequence identity to MMP1090 over essentially the entire length of the protein. Among these homologues, MMP1090 shares 33 and 32 % amino acid identity with two studied archaeal UDP-glucose 4-epimerases, from the hyperthermophiles Pyrobaculum calidifontis (Sakuraba et al 2011) and Pyrococcus horikoshii (Chung et al 2012). In support of the annotation, several signature motifs or amino acid residues possessed by UDP-glucose 4-epimerases are also found in MMP1090, including an YxxxK motif and a glycine-rich motif (Kallberg et al 2002;Persson and Kallberg 2013).…”

Section: Discussionmentioning

confidence: 71%

Identification of a gene involved in the biosynthesis pathway of the terminal sugar of the archaellin N-linked tetrasaccharide in Methanococcus maripaludis

Ding

Jones

Brimacombe

et al. 2015

Antonie van Leeuwenhoek

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In Methanococcus maripaludis, the three archaellins which comprise the archaellum are modified at multiple sites with an N-linked tetrasaccharide with the structure of Sug-4-β-ManNAc3NAmA6Thr-4-β-GlcNAc3NAcA-3-β-GalNAc, where Sug is a unique sugar (5S)-2-acetamido-2,4-dideoxy-5-O-methyl-L-erythro-hexos-5-ulo-1,5-pyranose, so far found exclusively in this species. In this study, a six-gene cluster mmp1089-1094, neighboring one of the genomic regions already known to contain genes involved with the archaellin N-glycosylation pathway, was examined for its potential involvement in the archaellin N-glycosylation or sugar biosynthesis pathway. The co-transcription of these six genes was demonstrated by RT-PCR. Mutants carrying an in-frame deletion in mmp1090, mmp1091 or mmp1092 were successfully generated. The Δmmp1090 deletion mutant was archaellated when examined by electron microscopy and mass spectrometry analysis of purified archaella showed that the archaellins were modified with a truncated N-glycan in which the terminal sugar residue and the threonine linked to the third sugar residue were missing. Both gene annotation and bioinformatic analyses indicate that MMP1090 is a UDP-glucose 4-epimerase, suggesting that the unique terminal sugar of the archaellin N-glycan might be synthesised from UDP-glucose or UDP-N-acetylglucosamine with an essential early step in synthesis catalysed by MMP1090. In contrast, no detectable phenotype related to archaellin glycosylation was observed in mutants deleted for either mmp1091 or mmp1092 while attempts to delete mmp1089, mmp1093 and mmp1094 were unsuccessful. Based on its demonstrated involvement in the archaellin N-glycosylation pathway, we designated mmp1090 as aglW.

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Crystal structure of UDP-galactose 4-epimerase from the hyperthermophilic archaeon Pyrobaculum calidifontis

Cited by 28 publications

References 29 publications

Altered cofactor binding affects stability and activity of human UDP-galactose 4′-epimerase: Implications for type III galactosemia

Altered cofactor binding affects stability and activity of human UDP-galactose 4′-epimerase: Implications for type III galactosemia

Binding of NAD+ and l-Threonine Induces Stepwise Structural and Flexibility Changes in Cupriavidus necator l-Threonine Dehydrogenase

Identification of a gene involved in the biosynthesis pathway of the terminal sugar of the archaellin N-linked tetrasaccharide in Methanococcus maripaludis

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