Auxiliary Activity Family 3

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• Author: ^^^Roland Ludwig^^^
• Responsible Curator: ^^^Roland Ludwig^^^

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Auxiliary Activity Family AA3
Clan	GH-x
Mechanism	retaining/inverting
Active site residues	known/not known
CAZy DB link
https://www.cazy.org/AA3.html

Familiy members

AA3 members have been divided into three subfamilies based on activity.

Subfamily 1 - CDH

Kinetics and Mechanism

Cellobiose dehydrogenases (CDHs) are secreted flavocytochromes exclusively found in wood-degrading and phytopathogenic fungi belonging to the phyla Basidiomycota (Class-I CDHs) and Ascomycota (Class-II and -III CDHs).

CDHs oxidize a wide variety of lignocellulose-derived saccharides to their corresponding sugar lactones. They show a high preference for soluble, β-(1,4)-interlinked saccharides, but scarcely oxidize monosaccharides. Highest catalytic efficiencies are observed for β-D-cellobiose, the dimeric subunit of cellulose, and higher soluble cellooligosaccharides. Hemicellulose- and starch- derived oligosaccharides, such as xylo- or manno or maltooligosaccharides are oxidized by a number of CDHs, although with lower catalytic efficiencies.

A common feature of all CDHs is their complex bipartite structure, which comprises a C-terminal cytochrome-binding fragment (CYT) and a larger, catalytic flavodehydrogenase (DH) domain encoded within a single polypeptide chain. Both domains are connected by a linear, papain-sensitive linker peptide which typically comprises 15 – 20 amino acids. Substrate oxidation occurs in the DH domain, where substrates bind in the active site with the C1 carbon (corresponding to the reducing ends) facing the N5 atom of the isoalloxazine ring at a distance of approx. 2.9 Å. This orientation allows oxidative attack of cellobiose by a catalytic histidine in the vicinity of C1 by a general hydride transfer mechanism, in which the catalytic His initially abstracts a proton from the C1 hydroxyl group. Transfer of the anomeric (C1) hydrogen to the N5 atom of the FAD cofactor then results in a 2-electron reduced FAD (hydroquinone form), while cellobiose is oxidized to cellobionolactone.

Rapid kinetic techniques showed that mixing of CDH with cellobiose resulted in rapid reduction of the FAD cofactor, followed by a slower interdomain electron transfer to the heme b moiety [1,2]. The idea of a sequential electron transfer chain from FAD to CYT was further strengthened by the observation that the oxidative potential of the heme b is always higher than that of the flavin. An important in vivo function of CDH is the reduction and activation of lytic polysaccharide monooxygenases belonging to family AA9 in the CAZy classification.

Catalytic Residues

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Three-dimensional structures

The crystal structure of the isolated CYT domain from P. chrysosporium CDH was reported in 2000 at a resolution of 1.9 Å (pdb: 1D7C) (Hallberg et al., 2000). The fragment folds into a compact globular structure which resembles the antibody fold of the heavy-chain Fab fragment. The propionate arm of the heme b is partly solvent exposed. The heme iron is hexa-coordinated by Met and His as axial ligands (Cox et al., 1992). The crystal structure of the P. chrysosporium DH domain (1.6 Å resolution, pdb: 1KDG) was reported in 2002. The flavin binding domain features a typical, flavin-binding βαβ-motif, the Rossman-fold. The FAD moiety is non-covalently bound to the enzyme. Recently, full-length structures of Neurospora crassa and Myriococcum thermophilum CDHs were reported. Two structures of N. crassa CDH showed an “open” conformation in which DH and CYT were spatially separated, whereas a structure of M. thermophilum CDH showed a “closed” conformation. Analysis by SAXS also suggested a number of possible intermediate conformers that exist in solution. While the “closed” conformation allows interdomain electron transfer from DH to CYT, reduction of electron acceptors (e.g. AA9 enzymes) might occur in the open conformation, in which the heme cofactor is fully accessible.

Family Firsts

First stereochemistry determination

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First catalytic nucleophile identification

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First general acid/base residue identification

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First 3-D structure

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First CDH identified

CDH was first purified in 1974 from the wood-degrading degrading fungus Phanerochaete chrysosporium [3].

First demonstration of interaction with AA9

Interaction between CDH and LPMO was first published in patent application https://www.google.com/patents/US20100159536, and later published in more detail [4].

Fist 3-D structure

In 2000 and 2003 crystal structures of the isolated CYT and DH domain from Phanerochaete chrysosporium CDH were reported [5,6]. In 2015, the first structures of full-length CDHs were resolved [7]..

Subfamily 2 - P2O

Kinetics and Mechanism

P2O (pyranose:oxygen 2-oxidoreductase) is widespread in lignin-degrading, white-rot fungi and catalyzes the oxygen-dependent oxidation of several monosaccharides at the C2 position to yield the corresponding 2-keto-aldoses and H2O2 [8]. The preferred substrate is D-glucose, which is oxidized to 2-keto-D-glucose. The FAD cofactor in P2O is covalently linked through a histidyl linkage. The supposed physiological role of P2O is to generate H2O2, which is a substrate for lignin-degrading peroxidases. P2Os are localized in the hyphal periplasmatic space [9].

During the reductive half reaction, 2 electrons are transferred from the substrate to the FAD, leading to the formation of FADH2 and a 2-keto sugar. During the oxidative half reaction, reduction equivalents are transferred to molecular oxygen to yield H2O2. The catalytic reaction can be classified as a ping-pong bi-bi type, since the 2-keto-sugar product is released prior to the reaction with oxygen. P2O is the only known flavin-dependent oxidase which generates a C4a-hydroperoxy-flavin intermediate during the oxidative half-reaction [10]. Unlike other GMC enzymes, the FAD in P2O is covalently linked via its 8α-methyl group to the N12 atom of His167. The active site contains a conserved, catalytic His–Asn pair positioned below the FAD isoalloxazine ring, which is typical for GMC oxidoreductases. His is the catalytic base that facilitates deprotonation of the sugar substrate.

Catalytic Residues

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Three-dimensional structures

Several crystal structure of P2O from P. chrysosporium and Trametes multicolor with various ligands are available in the pdb database. P2Os are homotetrameric enzymes with native molecular masses of approx. 270 kDa containing 4 flavin-binding Rossmann domains of class α/β typical for GMC oxidoreductases. The substrate-binding subdomain has a six-stranded central β sheet and three α helices. The homotetramer conceals a large internal cavity, from which the four active sites are accessible. Four substrate channels lead from the protein surface to the active sites.

Family Firsts

First stereochemistry determination

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First catalytic nucleophile identification

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First general acid/base residue identification

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First 3-D structure

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First P2O identified

Pyranose oxidase was first isolated from the basidiomycete Polyporus obtusus in 1968 [11].

First 3-D structure

P2O from Trametes multicolor MB 49 (pdb: 1TT0; [12])

Subfamily 3 - GO

Kinetics and Mechanism

Glucose oxidase catalyzes the regioselective oxidation of β-D-glucose to gluconic acid by utilizing molecular oxygen as an electron acceptor with simultaneous production of hydrogen peroxide. Glucose oxidases are produced by a number of fungi and insects. Proposed functions are related to the peroxide-producing abilities of the enzyme and include the preservation of honey, microbial defense as well as the support of H2O2 dependent ligninases in wood degrading fungi [13].

In the oxidative half reaction of GOx, two-electron oxidation of D-glucose at C1 results in the formation of gluconolactone and reduced cofactor (FADH2). Reduction by glucose occurs via a hydride ion transfer to the N-5 position of the FAD. Oxygen reduction to H2O2 involves the uptake of two electrons (from FADH2) and two protons. A highly conserved His (His516 in Aspergillus niger GOx) in the active site of the enzyme was identified by site directed mutagenesis as the catalytic base [14].

Catalytic Residues

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Three-dimensional structures

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Family Firsts

First stereochemistry determination

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First catalytic nucleophile identification

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First general acid/base residue identification

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First 3-D structure

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First GOx identified

Glucose oxidase from Aspergillus niger in 1928 (Müller D (1928) Oxidation von Glukose mit Extrakten aus Aspegillus niger. Biochem Z 199:136–170)

First 3-D structure

Glucose oxidase from Aspergillus niger ([15], pdb code 1GAL)

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Authors may get an idea of what to put in each field from Curator Approved Glycoside Hydrolase Families. (TIP: Right click with your mouse and open this link in a new browser window...)

In the meantime, please see these references for an essential introduction to the CAZy classification system: [1, 2].

References

1. Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. The Biochemist, vol. 30, no. 4., pp. 26-32. Download PDF version.

2. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, and Henrissat B. (2009). The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 2009;37(Database issue):D233-8. DOI:10.1093/nar/gkn663 |