Klaus Piontek

High-resolution native and complex structures of thermostable beta-mannanase from Thermomonospora fusca - substrate specificity in glycosyl hydrolase family 5.

BACKGROUND . beta-Mannanases hydrolyse the O-glycosidic bonds in mannan, a hemicellulose constituent of plants. These enzymes have potential use in pulp and paper production and are of significant biotechnological interest. Thermostable beta-mannanases would be particularly useful due to their high temperature optimum and broad pH tolerance. The thermophilic actinomycete Thermomonospora fusca secretes at least one beta-mannanase (molecular mass 38 kDa) with a temperature optimum of 80 degreesC. No three-dimensional structure of a mannan-degrading enzyme has been reported until now. RESULTS . The crystal structure of the thermostable beta-mannanase from T. fusca has been determined by the multiple isomorphous replacement method and refined to 1.5 A resolution. In addition to the native enzyme, the structures of the mannotriose- and mannohexaose-bound forms of the enzyme have been determined to resolutions of 1.9 A and 1.6 A, respectively. CONCLUSIONS . Analysis of the -1 subsite of T. fusca mannanase reveals neither a favourable interaction towards the axial HO-C(2) nor a discrimination against the equatorial hydroxyl group of gluco-configurated substrates. We propose that selectivity arises from two possible mechanisms: a hydrophobic interaction of the substrate with Val263, conserved in family 5 bacterial mannanases, which discriminates between the different conformations of the hydroxymethyl group in native mannan and cellulose; and/or a specific interaction between Asp259 and the axial hydroxyl group at the C(2) of the substrate in the -2 subsite. Compared with the catalytic clefts of family 5 cellulases, the groove of T. fusca mannanase has a strongly reduced number of aromatic residues providing platforms for stacking with the substrate. This deletion of every second platform is in good agreement with the orientation of the axial hydroxyl groups in mannan.

Do carbohydrates play a role in the lignin peroxidase cycle? Redox catalysis in the endergonic region of the driving force.

The redox cycle of lignin peroxidase (LiP) is discussed in terms of the Marcus theory of electron transfer. The difference in kinetic behaviour of the two redox couples LiP-Compound I/LiP-Compound II (LiPI/LiPII), respectively LiPII/LiP, in the oxidation of veratryl alcohol is attributed to an estimated increase in reorganization energy of about 0.5 eV for the conversion of LiPII to native enzyme compared to the reduction of LiPI to LiPII. Whereas LiPI/LiPII involves a transition from a low-spin oxyferryl prophyrin radical cation to a low-spin oxyferryl porphyrin system, the conversion of LiPII to native enzyme involves a change in spin-state to high-spin ferric, accompanied by a conformational change of the protein. In addition, a molecule of water is formed after protonation of the oxyferryl porphyrin system by the distal His-47 and Arg-43. Furthermore, the reduction of LiPI to LiPII is observed as an irreversible process. Since the oxidation of veratryl alcohol by oxidized LiP will occur in the endergonic region of the driving force, it is postulated that the thermodynamic unfavourable formation of veratryl alcohol radical cation is facilitated by reaction of a nucleophile with the incipient radical cation. It is further postulated that the ordered carbohydrate residues found near the entrance to the active site channel in the LiP crystal structure play a role in this process.

Radical formation on a conserved tyrosine residue is crucial for DyP activity

Dye-decolorizing peroxidases (DyPs) are able to cleave bulky anthraquinone dyes. The recently published crystal structure of AauDyPI reveals that a direct oxidation in the distal heme cavity can be excluded for most DyP substrates. It is shown that a surface-exposed tyrosine residue acts as a substrate interaction site for bulky substrates. This amino acid is conserved in eucaryotic DyPs but is missing in the structurally related chlorite dismutases (Clds). Dye-decolorizing peroxidases of procaryotic origin equally possess a conserved tyrosine in the same region of the polypeptide albeit not at the homologous position.

Crystallization and Preliminary Crystallographic Analysis of two Beta-mannanase Isoforms from Thermomonospora fusca KW3

Three beta-mannanase isoforms were isolated from the supernatant of a thermophilic actinomycete culture from Thermomonospora fusca KW3. Two of the isoforms (Q1, Q 1.1) were crystallized by the hanging-drop method at room temperature using ammonium sulfate as a precipitant. The isoforms form rod-shaped colorless crystals. Both belong to the orthorhombic space group P2(1)2(1)2(1). The cell dimensions are a = 46.7, b = 61.1, and c = 128.2 A for isoform Q1, and a = 43.8, b = 46.2, and c = 132.8 A for isoform Q1.1. The asymmetric unit of either isoform contains one mannanase molecule. Native data have been collected to 2.2 A resolution for Q1 and to 1.65 A resolution for Q1.1 using synchrotron radiation.

Structure elucidation of β-mannanase: from the electron-density map to the DNA sequence

The crystal structure of affinity-purified Thermomonospora fusca beta-mannanase has been solved despite the lack of the major part of the amino-acid sequence. A high-quality electron-density map allowed the identification of a stretch of eight amino acids close to the C-terminus which was used to design a degenerate downstream PCR primer. Together with a specific primer previously derived from the N-terminus, 95.7% of the mannanase gene sequence was obtained from genomic T. fusca DNA by PCR. The structure-derived sequence was then compared with the DNA-derived sequence and corrected when necessary. Applying the presented protocol, there was no need to manually build a model at an early stage of structure determination, an erroneous and tedious process, especially in the absence of the amino-acid sequence. Using the DNA sequence information and the current version of ARP/wARP, 281 residues, or 93% of the polypeptide chain (including side chains), were built and refined to an R factor of 16.5% without any manual intervention.