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The molecular architecture of QdtA, a sugar 3,4-ketoisomerase from Thermoanaerobacterium thermosaccharolyticum.

ABSTRACT: Unusual di- and trideoxysugars are often found on the O-antigens of Gram-negative bacteria, on the S-layers of Gram-positive bacteria, and on various natural products. One such sugar is 3-acetamido-3,6-dideoxy-D-glucose. A key step in its biosynthesis, catalyzed by a 3,4-ketoisomerase, is the conversion of thymidine diphosphate (dTDP)-4-keto-6-deoxyglucose to dTDP-3-keto-6-deoxyglucose. Here we report an X-ray analysis of a 3,4-ketoisomerase from Thermoanaerobacterium thermosaccharolyticum. For this investigation, the wild-type enzyme, referred to as QdtA, was crystallized in the presence of dTDP and its structure solved to 2.0-Å resolution. The dimeric enzyme adopts a three-dimensional architecture that is characteristic for proteins belonging to the cupin superfamily. In order to trap the dTDP-4-keto-6-deoxyglucose substrate into the active site, a mutant protein, H51N, was subsequently constructed, and the structure of this protein in complex with the dTDP-sugar ligand was solved to 1.9-Å resolution. Taken together, the structures suggest that His 51 serves as a catalytic base, that Tyr 37 likely functions as a catalytic acid, and that His 53 provides a proton shuttle between the C-3' hydroxyl and the C-4' keto group of the hexose. This study reports the first three-dimensional structure of a 3,4-ketoisomerase in complex with its dTDP-sugar substrate and thus sheds new molecular insight into this fascinating class of enzymes.

SUBMITTER: Thoden JB

PROVIDER: S-EPMC4093945 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature

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The molecular architecture of QdtA, a sugar 3,4-ketoisomerase from Thermoanaerobacterium thermosaccharolyticum.

Thoden James B JB Holden Hazel M HM

Protein science : a publication of the Protein Society 20140325 6

Unusual di- and trideoxysugars are often found on the O-antigens of Gram-negative bacteria, on the S-layers of Gram-positive bacteria, and on various natural products. One such sugar is 3-acetamido-3,6-dideoxy-D-glucose. A key step in its biosynthesis, catalyzed by a 3,4-ketoisomerase, is the conversion of thymidine diphosphate (dTDP)-4-keto-6-deoxyglucose to dTDP-3-keto-6-deoxyglucose. Here we report an X-ray analysis of a 3,4-ketoisomerase from Thermoanaerobacterium thermosaccharolyticum. For ...[more]

PMID: 24616215

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Project description:BACKGROUND:?-Glucosidase is an important component of the cellulase enzyme system. It does not only participate in cellulose degradation, it also plays an important role in hydrolyzing cellulose to fermentable glucose by relieving the inhibition of exoglucanase and endoglucanase from cellobiose. Therefore, the glucose-tolerant ?-glucosidase with high specific activity for cellobiose might be a potent candidate for industrial applications. RESULTS:The ?-glucosidase gene bgl that encodes a 443-amino-acid protein was cloned and over-expressed from Thermoanaerobacterium thermosaccharolyticum DSM 571 in Escherichia coli. The phylogenetic trees of ?-glucosidases were constructed using Neighbor-Joining (NJ) and Maximum-Parsimony (MP) methods. The phylogeny and amino acid analysis indicated that the BGL was a novel ?-glucosidase. By replacing the rare codons for the N-terminal amino acids of the target protein, the expression level of bgl was increased from 6.6 to 11.2 U/mg in LB medium. Recombinant BGL was purified by heat treatment followed by Ni-NTA affinity. The optimal activity was at pH 6.4 and 70°C. The purified enzyme was stable over pH range of 5.2-7.6 and had a 1 h half life at 68°C. The activity of BGL was significantly enhanced by Fe2+ and Mn2+. The Vmax of 64 U/mg and 120 U/mg were found for p-nitrophenyl-?-D-glucopyranoside (Km value of 0.62?mM) and cellobiose (Km value of 7.9?mM), respectively. It displayed high tolerance to glucose and cellobiose. The Kcat for cellobiose was 67.7?s-1 at 60°C and pH 6.4, when the concentration of cellobiose was 290?mM. It was activated by glucose at concentrations lower that 200?mM. With glucose further increasing, the enzyme activity of BGL was gradually inhibited, but remained 50% of the original value in even as high as 600?mM glucose. CONCLUSIONS:The article provides a useful novel ?-glucosidase which displayed favorable properties: high glucose and cellobiose tolerance, independence of metal ions, and high hydrolysis activity on cellobiose.

Project description:BACKGROUND:Energy shortage and environmental pollution are two severe global problems, and biological hydrogen production from lignocellulose shows great potential as a promising alternative biofuel to replace the fossil fuels. Currently, most studies on hydrogen production from lignocellulose concentrate on cellulolytic microbe, pretreatment method, process optimization and development of new raw materials. Due to no effective approaches to relieve the inhibiting effect of inhibitors, the acid pretreated lignocellulose hydrolysate was directly discarded and caused environmental problems, suggesting that isolation of inhibitor-tolerant strains may facilitate the utilization of acid pretreated lignocellulose hydrolysate. RESULTS:Thermophilic bacteria for producing hydrogen from various kinds of sugars were screened, and the new strain named MJ1 was isolated from paper sludge, with 99% identity to Thermoanaerobacterium thermosaccharolyticum by 16S rRNA gene analysis. The hydrogen yields of 11.18, 4.25 and 2.15 mol-H2/mol sugar can be reached at an initial concentration of 5 g/L cellobiose, glucose and xylose, respectively. The main metabolites were acetate and butyrate. More important, MJ1 had an excellent tolerance to inhibitors of dilute-acid (1%, g/v) pretreated sugarcane bagasse hydrolysate (DAPSBH) and could efficiently utilize DAPSBH for hydrogen production without detoxication, with a production higher than that of pure sugars. The hydrogen could be quickly produced with the maximum hydrogen production reached at 24 h. The hydrogen production reached 39.64, 105.42, 111.75 and 110.44 mM at 20, 40, 60 and 80% of DAPSBH, respectively. Supplementation of CaCO3 enhanced the hydrogen production by 21.32% versus the control. CONCLUSIONS:These results demonstrate that MJ1 could directly utilize DAPSBH for biohydrogen production without detoxication and can serve as an excellent candidate for industrialization of hydrogen production from DAPSBH. The results also suggest that isolating unique strains from a particular environment offers an ideal way to conquer the related problems.

Dataset Information

The molecular architecture of QdtA, a sugar 3,4-ketoisomerase from Thermoanaerobacterium thermosaccharolyticum.

Publications

The molecular architecture of QdtA, a sugar 3,4-ketoisomerase from Thermoanaerobacterium thermosaccharolyticum.

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