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Cellobiose dehydrogenase: An essential enzyme for lignocellulose degradation in nature – A review / Cellobiosedehydrogenase: Ein essentielles Enzym für den Lignozelluloseabbau in der Natur – Eine Übersicht

Daniel Kracher
Daniel Kracher
 et 
Roland Ludwig
Roland Ludwig
   | 02 déc. 2016
Die Bodenkultur: Journal of Land Management, Food and Environment's Cover Image
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Article Category: Research Article
Publié en ligne: 02 déc. 2016
Pages: 145 - 163
Reçu: 03 mai 2016
Accepté: 29 août 2016
DOI: https://doi.org/10.1515/boku-2016-0013
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© 2016 De Gruyter, www.degruyter.com/view/j/boku
This article is distributed under the terms of the Creative Commons Attribution Non-Commercial License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Unrooted phylogenetic tree comprising 27 cellobiose dehydrogenases (Ungewurzelter phylogenetischer Stammbaum von 27 Cellobiosedehydrogenasen). CDH sequences were derived from the NCBI database (http://www.ncbi.nlm.nih.gov/protein). Signal sequences were identified using the SignalP 4.1 server (http://www.cbs.dtu.dk/services/SignalP) and removed before further analysis. Evolutionary relationships were inferred with the minimum-evolution method (Rzhetsky and Nei, 1992) using the MEGA 7 software package (http://www.megasoftware.net). The tree was generated by the neighbor-joining method and the bootstrap consensus tree was inferred from 1000 replicates.
Unrooted phylogenetic tree comprising 27 cellobiose dehydrogenases (Ungewurzelter phylogenetischer Stammbaum von 27 Cellobiosedehydrogenasen). CDH sequences were derived from the NCBI database (http://www.ncbi.nlm.nih.gov/protein). Signal sequences were identified using the SignalP 4.1 server (http://www.cbs.dtu.dk/services/SignalP) and removed before further analysis. Evolutionary relationships were inferred with the minimum-evolution method (Rzhetsky and Nei, 1992) using the MEGA 7 software package (http://www.megasoftware.net). The tree was generated by the neighbor-joining method and the bootstrap consensus tree was inferred from 1000 replicates.

Structures and kinetic mechanism of cellobiose dehydrogenase (Strukturen und kinetischer Mechanismus von Cellobiosedehydrogenase). (A) Crystal structures of full-length CDHs from N. crassa (pdb: 4QI7) and M. thermophilum (pdb: 4QI6). Shown are the relative orientations of the cytochrome (CYT) domains (red), the dehydrogenase (DH) domains (yellow) and the linker peptides (grey) in the “open” state of two N. crassa CDHs (“mol A” and “mol B”) in comparison to the “closed” state of M. thermophilum CDH. Note the different orientations of the CYT domains in the structures of N. crassa. Family 1 carbohydrate binding modules (CBM1s) are shown in green. (B) Active--site architecture of M. thermophilum CDH (yellow) in comparison to the CBLM-bound DH (grey; pdb: 4QI5) and ligand-free DH (green; pdb: 4QI4). Figure modified from Tan et al. (2015). The propionate-A chain of CYT is approx. 9 Å away from the FAD. (C) Proposed catalytic hydride-transfer mechanism of CDH. Indicated is the suggested catalytic histidine. Bound substrates are eventually converted to a lactone. Numbering of amino acids is for M. thermophilum CDH. Figure adapted from Wongnate and Chaiyen (2013).
Structures and kinetic mechanism of cellobiose dehydrogenase (Strukturen und kinetischer Mechanismus von Cellobiosedehydrogenase). (A) Crystal structures of full-length CDHs from N. crassa (pdb: 4QI7) and M. thermophilum (pdb: 4QI6). Shown are the relative orientations of the cytochrome (CYT) domains (red), the dehydrogenase (DH) domains (yellow) and the linker peptides (grey) in the “open” state of two N. crassa CDHs (“mol A” and “mol B”) in comparison to the “closed” state of M. thermophilum CDH. Note the different orientations of the CYT domains in the structures of N. crassa. Family 1 carbohydrate binding modules (CBM1s) are shown in green. (B) Active--site architecture of M. thermophilum CDH (yellow) in comparison to the CBLM-bound DH (grey; pdb: 4QI5) and ligand-free DH (green; pdb: 4QI4). Figure modified from Tan et al. (2015). The propionate-A chain of CYT is approx. 9 Å away from the FAD. (C) Proposed catalytic hydride-transfer mechanism of CDH. Indicated is the suggested catalytic histidine. Bound substrates are eventually converted to a lactone. Numbering of amino acids is for M. thermophilum CDH. Figure adapted from Wongnate and Chaiyen (2013).

Electron-chain model for electron transfer in CDH (Das Elektronenketten-Modell für den Elektronentransfer in CDH). Following substrate oxidation, electrons are transferred sequentially from the reduced flavin to the heme cofactor and eventually to a suitable electron acceptor such as LPMO. FADH, flavin semiquinone. Figure adapted from Henriksson et al. (2000).
Electron-chain model for electron transfer in CDH (Das Elektronenketten-Modell für den Elektronentransfer in CDH). Following substrate oxidation, electrons are transferred sequentially from the reduced flavin to the heme cofactor and eventually to a suitable electron acceptor such as LPMO. FADH, flavin semiquinone. Figure adapted from Henriksson et al. (2000).

Structure of lytic polysaccharide monooxygenases (Struktur von lytischen Polysaccharid-Monooxygenasen, LPMOs). (A) N. crassa LPMO9F modeled onto an artificial cellulose surface. The active-site copper is shown in blue. Conserved aromatic amino acids on the surface are indicated in pink. The inset shows the copper coordination with the typical “histidine brace” formed by His1 and His72. (B) Sequence alignment of 18 crystallized and putative LPMOs from basidiomycetes and ascomycetes. The suggested “PGP” docking patch for CDH is highlighted in pink. The sequence alignment was generated using MUSCLE.
Structure of lytic polysaccharide monooxygenases (Struktur von lytischen Polysaccharid-Monooxygenasen, LPMOs). (A) N. crassa LPMO9F modeled onto an artificial cellulose surface. The active-site copper is shown in blue. Conserved aromatic amino acids on the surface are indicated in pink. The inset shows the copper coordination with the typical “histidine brace” formed by His1 and His72. (B) Sequence alignment of 18 crystallized and putative LPMOs from basidiomycetes and ascomycetes. The suggested “PGP” docking patch for CDH is highlighted in pink. The sequence alignment was generated using MUSCLE.

Suggested substrate cycling during oxidative cellulolysis by wood decaying fungi (Substratkreislauf während des oxidativen Zelluloseabbaus durch holzabbauende Pilze). Cellulose-derived oligosaccharides, hemicellulose-derived xylo- and manno-oligosaccharides and starch-derived malto-oligosaccharides are substrates for a number of CDHs, and can be released by the action of LPMO and hydrolases.
Suggested substrate cycling during oxidative cellulolysis by wood decaying fungi (Substratkreislauf während des oxidativen Zelluloseabbaus durch holzabbauende Pilze). Cellulose-derived oligosaccharides, hemicellulose-derived xylo- and manno-oligosaccharides and starch-derived malto-oligosaccharides are substrates for a number of CDHs, and can be released by the action of LPMO and hydrolases.

Kinetic properties of CDHs from various sources (Kinetische Eigenschaften von CDHs unterschiedlicher Herkunft). All values were determined with dichloroindophenol (DCIP) as terminal electron acceptor, with the exception of the N. crassa CDHs IIA and IIB, for which benzoquinone was used.

CellobioseXylobioseMaltoseGlucose
Source of CDHkcatKMkcatKMkcatKMkcatKMpHReferences
Class I
   Phanerochaete chrysosporium160.11001.12402.616004.5Henriksson et al., 1998
   Trametes villosa240.21177.72.13501.913004.5Ludwig et al., 2003
   Sclerotium rolfsii270.12275.40.82401.512503.5Baminger et al., 2001
   Trametes hirsuta110.04002.8

recombinantly produced enzyme

n.d.1.0

recombinantly produced enzyme

n.d.5.0Nakagame et al., 2006
   Ceriporiopsis subvermispora250.14n.d.1.33001.033004.5Harreither et al., 2009
   Schizophyllum commune130.03n.d.00004.5Fang et al., 1998
   Cerrena unicolor190.29n.d.n.d.004.5Sulej et al., 2015
   Coprinopsis cinerea970.16n.d.n.d.34.43545.0Turbe-Doan et al., 2013
Class II
   Humicola insolens140.053.07.11.77.6007.0Schou et al., 1998
   Neurospora crassa IIA

kcat, (s−1); KM, (mM); n.d., not determined

460.09453.60.4175537006.0Sygmund et al., 2012
   Neurospora crassa IIB

kcat, (s−1); KM, (mM); n.d., not determined

110.025.81.33.53.48.15506.0Sygmund et al., 2012
   Thielavia terrestris1.20.04n.d.0.22.51546.0Langston et al., 2012
   Myriococcum thermophilum

kcat, (s−1); KM, (mM); n.d., not determined

130.01n.d.1.211142506.0Zámocký et al., 2008
   Corynascus thermophilus130.08n.d.n.d.13937.5Harreither et al., 2012
   Podospora anserina8.60.13n.d.n.d.1.63296.0Turbe-Doan et al., 2013

Literature overview of in vitro assays demonstrating the synergy of LPMO and CDH (Literaturübersicht über in vitro Analysen, die den Synergismus zwischen LPMO und CDH verdeutlichen).

CDHLPMOSubstrateCellulaseReference
OrganismNameOrganismName
H. insolensHiCDHT. aurantiacusTaGH61APASC, MC+Langston et al., 2011
T. terrestrisTtCDHT. terrestrisTtGH61EPASC,MC+Langston et al., 2011
M. thermophilaMtCDH-2N. crassaNCU01050PASC-Phillips et al., 2011b
M. thermophilaMtCDH-2N. crassaNCU07898PASC-Phillips et al., 2011b
M. thermophilaMtCDH-2N. crassaNCU08760PASC-Phillips et al., 2011b
T. terrestrisTtCDHT. aurantiacusTaGH61APASC+Langston et al., 2012
N. crassaCDH IIAN. crassaNCU01867MC-Kittl et al., 2012
N. crassaCDH IIAN. crassaNcLPMO9CMC-Kittl et al., 2012
N. crassaCDH IIAN. crassaNcLPMO9FMC-Kittl et al., 2012
N. crassaCDH IIAN. crassaNCU08760MC-Kittl et al., 2012
P. cinnabarinusPcCDHP. anserinaPaLPMO9APASC-Bey et al., 2013
P. cinnabarinusPcCDHP. anserinaPaLPMO9BPASC-Bey et al., 2013
M. thermophilumMtCDHN. crassaNcLPMO9CCellopentaose-Isaksen et al., 2014
M. thermophilaMtCDH-2N. crassaNCU08746Amylopectin-Vu et al., 2014
P. anserinaPaCDHBP. anserinaPaLPMO9APASC-Bennati-Granier et al., 2015
P. anserinaPaCDHBP. anserinaPaLPMO9EPASC-Bennati-Granier et al., 2015
P. anserinaPaCDHBP. anserinaPaLPMO9HPASC-Bennati-Granier et al., 2015
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