scholarly journals Structural and Electronic Snapshots during the Transition from a Cu(II) to Cu(I) Metal Center of a Lytic Polysaccharide Monooxygenase by X-ray Photoreduction

2014 ◽  
Vol 289 (27) ◽  
pp. 18782-18792 ◽  
Author(s):  
Mikael Gudmundsson ◽  
Seonah Kim ◽  
Miao Wu ◽  
Takuya Ishida ◽  
Majid Hadadd Momeni ◽  
...  
2015 ◽  
Vol 71 (11) ◽  
pp. 1448-1452 ◽  
Author(s):  
John-Paul Bacik ◽  
Sophanit Mekasha ◽  
Zarah Forsberg ◽  
Andrey Kovalevsky ◽  
Jay C. Nix ◽  
...  

Bacteria and fungi express lytic polysaccharide monooxgyenase (LPMO) enzymes that act in conjunction with canonical hydrolytic sugar-processing enzymes to rapidly convert polysaccharides such as chitin, cellulose and starch to single monosaccharide products. In order to gain a better understanding of the structure and oxidative mechanism of these enzymes, large crystals (1–3 mm3) of a chitin-processing LPMO from the Gram-positive soil bacteriumJonesia denitrificanswere grown and screened for their ability to diffract neutrons. In addition to the collection of neutron diffraction data, which were processed to 2.1 Å resolution, a high-resolution room-temperature X-ray diffraction data set was collected and processed to 1.1 Å resolution in space groupP212121. To our knowledge, this work marks the first successful neutron crystallographic experiment on an LPMO. Joint X-ray/neutron refinement of the resulting data will reveal new details of the structure and mechanism of this recently discovered class of enzymes.


2019 ◽  
Vol 75 (4) ◽  
pp. 368-380 ◽  
Author(s):  
Octav Caldararu ◽  
Francesco Manzoni ◽  
Esko Oksanen ◽  
Derek T. Logan ◽  
Ulf Ryde

Neutron crystallography is a powerful method to determine the positions of H atoms in macromolecular structures. However, it is sometimes hard to judge what would constitute a chemically reasonable model, and the geometry of H atoms depends more on the surroundings (for example the formation of hydrogen bonds) than heavy atoms, so that the empirical geometry information for the H atoms used to supplement the experimental data is often less accurate. These problems may be reduced by using quantum-mechanical calculations. A method has therefore been developed to combine quantum-mechanical calculations with joint crystallographic refinement against X-ray and neutron data. A first validation of this method is provided by re-refining the structure of the galectin-3 carbohydrate-recognition domain in complex with lactose. The geometry is improved, in particular for water molecules, for which the method leads to better-resolved hydrogen-bonding interactions. The method has also been applied to the active copper site of lytic polysaccharide monooxygenase and shows that the protonation state of the amino-terminal histidine residue can be determined.


Biochemistry ◽  
2017 ◽  
Vol 56 (20) ◽  
pp. 2529-2532 ◽  
Author(s):  
John-Paul Bacik ◽  
Sophanit Mekasha ◽  
Zarah Forsberg ◽  
Andrey Y. Kovalevsky ◽  
Gustav Vaaje-Kolstad ◽  
...  

Amylase ◽  
2019 ◽  
Vol 3 (1) ◽  
pp. 41-54 ◽  
Author(s):  
Sebastian J. Muderspach ◽  
Tobias Tandrup ◽  
Kristian E. H. Frandsen ◽  
Gianluca Santoni ◽  
Jens-Christian N. Poulsen ◽  
...  

Abstract Lytic polysaccharide monooxygenases (LPMOs) are recently discovered copper enzymes that cleave recalcitrant polysaccharides by oxidation. The structure of an Aspergillus oryzae LPMO from the starch degrading family AA13 (AoAA13) has previously been determined from an orthorhombic crystal grown in the presence of copper, which is photoreduced in the structure. Here we describe how crystals reliably grown in presence of Zn can be Cu-loaded post crystallization. A partly photoreduced structure was obtained by severely limiting the X-ray dose, showing that this LPMO is much more prone to photoreduction than others. A serial synchrotron crystallography structure was also obtained, showing that this technique may be promising for further studies, to reduce even further photoreduction. We additionally present a triclinic structure of AoAA13, which has less occluded ligand binding site than the orthorhombic one. The availability of the triclinic crystals prompted new ligand binding studies, which lead us to the conclusion that small starch analogues do not bind to AoAA13 to an appreciable extent. A number of disordered conformations of the metal binding histidine brace have been encountered in this and other studies, and we have previously hypothesized that this disorder may be a consequence of loss of copper. We performed molecular dynamics in the absence of active site metal, and showed that the dynamics in solution differ somewhat from the disorder observed in the crystal, though the extent is equally dramatic.


2016 ◽  
Vol 82 (22) ◽  
pp. 6557-6572 ◽  
Author(s):  
Yuka Kojima ◽  
Anikó Várnai ◽  
Takuya Ishida ◽  
Naoki Sunagawa ◽  
Dejan M. Petrovic ◽  
...  

ABSTRACTFungi secrete a set of glycoside hydrolases and lytic polysaccharide monooxygenases (LPMOs) to degrade plant polysaccharides. Brown-rot fungi, such asGloeophyllum trabeum, tend to have few LPMOs, and information on these enzymes is scarce. The genome ofG. trabeumencodes four auxiliary activity 9 (AA9) LPMOs (GtLPMO9s), whose coding sequences were amplified from cDNA. Due to alternative splicing, two variants ofGtLPMO9A seem to be produced, a single-domain variant,GtLPMO9A-1, and a longer variant,GtLPMO9A-2, which contains a C-terminal domain comprising approximately 55 residues without a predicted function. We have overexpressed the phylogenetically distinctGtLPMO9A-2 inPichia pastorisand investigated its properties. Standard analyses using high-performance anion-exchange chromatography–pulsed amperometric detection (HPAEC-PAD) and mass spectrometry (MS) showed thatGtLPMO9A-2 is active on cellulose, carboxymethyl cellulose, and xyloglucan. Importantly, compared to other known xyloglucan-active LPMOs,GtLPMO9A-2 has broad specificity, cleaving at any position along the β-glucan backbone of xyloglucan, regardless of substitutions. Using dynamic viscosity measurements to compare the hemicellulolytic action ofGtLPMO9A-2 to that of a well-characterized hemicellulolytic LPMO,NcLPMO9C fromNeurospora crassarevealed thatGtLPMO9A-2 is more efficient in depolymerizing xyloglucan. These measurements also revealed minor activity on glucomannan that could not be detected by the analysis of soluble products by HPAEC-PAD and MS and that was lower than the activity ofNcLPMO9C. Experiments with copolymeric substrates showed an inhibitory effect of hemicellulose coating on cellulolytic LPMO activity and did not reveal additional activities ofGtLPMO9A-2. These results provide insight into the LPMO potential ofG. trabeumand provide a novel sensitive method, a measurement of dynamic viscosity, for monitoring LPMO activity.IMPORTANCECurrently, there are only a few methods available to analyze end products of lytic polysaccharide monooxygenase (LPMO) activity, the most common ones being liquid chromatography and mass spectrometry. Here, we present an alternative and sensitive method based on measurement of dynamic viscosity for real-time continuous monitoring of LPMO activity in the presence of water-soluble hemicelluloses, such as xyloglucan. We have used both these novel and existing analytical methods to characterize a xyloglucan-active LPMO from a brown-rot fungus. This enzyme,GtLPMO9A-2, differs from previously characterized LPMOs in having broad substrate specificity, enabling almost random cleavage of the xyloglucan backbone.GtLPMO9A-2 acts preferentially on free xyloglucan, suggesting a preference for xyloglucan chains that tether cellulose fibers together. The xyloglucan-degrading potential ofGtLPMO9A-2 suggests a role in decreasing wood strength at the initial stage of brown rot through degradation of the primary cell wall.


2021 ◽  
Vol 9 ◽  
Author(s):  
Damao Wang ◽  
Yanping Li ◽  
Yuting Zheng ◽  
Yves S. Y. Hsieh

Lytic polysaccharide monooxygenase (LPMO) is a newly discovered and widely studied enzyme in recent years. These enzymes play a key role in the depolymerization of sugar-based biopolymers (including cellulose, hemicellulose, chitin and starch), and have a positive significance for biomass conversion. LPMO is a copper-dependent enzyme that can oxidize and cleave glycosidic bonds in cellulose and other polysaccharides. Their mechanism of action depends on the correct coordination of copper ions in the active site. There are still difficulties in the analysis of LPMO activity, which often requires multiple methods to be used in concert. In this review, we discussed various LPMO activity analysis methods reported so far, including mature mass spectrometry, chromatography, labeling, and indirect measurements, and summarized the advantages, disadvantages and applicability of different methods.


Author(s):  
Urszula Jankiewicz ◽  
◽  
Arletta Kochańska-Jeziorska ◽  
Agnieszka Gałązka

This review focuses on the enzymatic breakdown of chitin, taking into account the latest scientific reports on the activity of lytic polysaccharide monooxygenase (LPMO). Chitin is a natural, abundant polysaccharide of great practical importance in the environment. However, the insolubility in water and the tightly packed crystalline structure of chitin pose a serious obstacle to enzymatic degradation. This substrate can be converted into soluble sugars by the action of glycosidic hydrolases (GH), also known as chitinases. LPMO could prove to be helpful in enzymatic processes that increase the rate of chitin depolymerisation by improving the availability of substrates for chitinases. The unique action of LPMO is based on the ability to catalyse the oxidative cleavage of glycosidic chains present in complex, resistant crystal networks of chitin, and this cleavage facilitates the subsequent action of glycolytic hydrolases.


2018 ◽  
Vol 57 (26) ◽  
pp. 7903-7903
Author(s):  
Yaxing Wang ◽  
Xuemiao Yin ◽  
Wei Liu ◽  
Jian Xie ◽  
Junfeng Chen ◽  
...  
Keyword(s):  
X Ray ◽  

2018 ◽  
Vol 20 (9) ◽  
pp. 2091-2100 ◽  
Author(s):  
Damao Wang ◽  
Jing Li ◽  
Germán Salazar-Alvarez ◽  
Lauren S. McKee ◽  
Vaibhav Srivastava ◽  
...  

The gene CCT67099 from Fusarium fujikuroi was shown to encode a novel enzyme from the Lytic Polysaccharide Monooxygenase (LPMO) Family AA11.


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