Molecule of the Month: Cellulases and Bioenergy

Powerful fungal enzymes break down cellulose during industrial production of ethanol from plant material.

Cel7A from Trichoderma reesei contains a carbohydrate-binding module (top) and a catalytic domain (bottom, with cellulose in tan) connected by a flexible linker. The carbohydrate-binding module contains several tyrosines (turquoise) and glycosylation (tan) that grip the surface of a cellulose fiber.
Cel7A from Trichoderma reesei contains a carbohydrate-binding module (top) and a catalytic domain (bottom, with cellulose in tan) connected by a flexible linker. The carbohydrate-binding module contains several tyrosines (turquoise) and glycosylation (tan) that grip the surface of a cellulose fiber.
Download high quality TIFF image
Petroleum-based fuels are diminishing and are a major contributor to climate change, so bioenergy researchers are looking to Nature to generate cleaner, renewable fuels to power our world. Ethanol is emerging as an attractive solution, both as a fuel and as an intermediate to produce sustainable aviation fuel. Alcoholic beverages have been produced since before recorded history by fermentation of sugars, and now, the same technology is being used to produce ethanol for use as fuel. Today, corn and sugar cane provide most of these sugars, but this is not an ideal process since it co-opts land that is amenable for food production and these crops are energy intensive to produce. Instead, bioenergy researchers are looking for ways to convert the cellulose in hardier non-food crops, such as switchgrass, poplar and cornstalks, into ethanol.

Disassembling Cellulose

Cellulose is composed of glucose molecules, however, they are locked together tightly into a tough, stable strand. It is created by cellulose synthase, which layers many cellulose strands into an even tougher fibril. So, industrial processes need to separate these strands and cut them into sugars before they can be fermented into ethanol. Typically, plant material is pretreated with aggressive processes such as chemicals and "steam explosion" that disrupt the plant cell walls and provide access to cellulose fibers. Then, a concoction of cellulase enzymes breaks the cellulose strands into individual sugars. The fungus Trichoderma reesei (also known as Hypocrea jecorina) is a common source of these cellulase enzymes. It was found in the Solomon Islands during World War II, growing on cotton canvas. Today it is widely used for bioethanol production, and for other tasks such as softening up denim in stonewashed jeans.

Science of Cellulases

Some cellulases contain two domains to help them degrade sturdy cellulose fibers, shown here from PDB entries 7cel and 2mwk. One domain has a long groove that is form-fitted to bind to the cellulose chain, straining one glucose-glucose bond and positioning it against the catalytic machinery for cleavage. The other domain binds to cellulose and ensures that the enzyme is always in the right place, allowing it to perform many cleavage reactions in rapid succession.
Cel61B, with tyrosine in turquoise, glycosylation in tan, and metal ion in magenta, and beta-glucosidase, with a sugar molecule in red in the active site.
Cel61B, with tyrosine in turquoise, glycosylation in tan, and metal ion in magenta, and beta-glucosidase, with a sugar molecule in red in the active site.
Download high quality TIFF image

Cellulase Cocktails

Fungi like Trichoderma reesei secrete a complex cocktail of cellulose-degrading enzymes that work together to attack cellulose fibers. Two examples are included here, and structures of many others are available in the PDB archive. Cel61B, also known as endoglucanase 7, takes an aggressive approach, using a metal ion to generate reactive forms of oxygen that attack cellulose (PDB ID 2vtc). Similar to the cellulose-binding domain of Cel7A, it has several tyrosines and glycosylation to help glue it to the cellulose fiber. Beta-glucosidase (PDB ID 3zyz) works later in the process to clip short fragments of cellulose into individual glucose sugars.

Exploring the Structure

Cellulases

Cellulases use many molecular tricks to streamline their function. As seen above, they often have domains or surfaces that bind to the surface of cellulose fibers. The shape of the cellulose-binding site is also tuned to perform a specialized function. In Cel7A (PDB ID 4c4c), several loops embrace the cellulose strand, forming a tunnel with the active site at one end. Because of this, Cel7A cleaves small two-sugar fragments from the end of the cellulose fiber. However, Cel7B (endogluconase EG-1, PDB ID 1eg1) is missing these loops and has an open groove that can bind to cellulose chains anywhere along their length, allowing it to cleave cellulose in the middle of a chain. The close-up picture at right shows another molecular trick: these enzymes often distort one sugar ring (shown here in brighter pinks) into a less-stable conformation. This distortion helps activate the connecting oxygen (in red) for the cleavage reaction catalyzed by two glutamates (turquoise). Click on the image to explore these structures in an interactive JSmol. Note that the cellulose chain from PDB ID 4c4c is displayed for both proteins.

Topics for Further Discussion

  1. You can find many other structures of cellulases by using the EC number in the Annotation Browser for 3.2.1.4 (cellulases) and 3.2.1.91 (cellulose 1,4-beta-cellobiosidases).
  2. To see the flexible loop that connects the two domains in Cel7A, look at AF_AFP62694F1, the structure predicted by AlphaFold2. Notice that there are several prolines at the ends of the linker, to help with flexibility, and many threonines and serines that may be glycosylated.
  3. A quick warning about the science of cellulases: there are many different types of cellulases and scientists love to classify and name things. So, you’ll often find many different names for the same enzyme. For example, the short name Cel7A is based on a large-scale classification of cellulase families, and longer names like 1,4-beta-D-glucan cellobiohydrolase I or cellulose 1,4-beta cellobiosidase or exoglucanase I describe its action of cutting two-sugar units from the end of a cellulose strand.

Related PDB-101 Resources

References

  1. Robak, K., Balcerek, M. (2020) Current state-of-the-art in ethanol production from lignocellulosic feedstocks. Microbiol Res 240: 126534
  2. 2mwk: Happs, R.M., Guan, X., Resch, M.G., Davis, M.F., Beckham, G.T., Tan, Z., Crowley, M.F. (2015) O-glycosylation effects on family 1 carbohydrate-binding module solution structures. FEBS J 282: 4341-4356
  3. Payne, C.M., Knott, B.C., Mayes, H.B., Hansson, H., Himmel, M.E., Sandgren, M., Stahlberg, J., Beckham, G.T. (2015) Fungal cellulases. Chem Rev 115: 1308-1448
  4. 3zyz: Karkehabadi, S., Helmich, K.E., Kaper, T., Hansson, H., Mikkelsen, N.E., Gudmundsson, M., Piens, K., Fujdala, M., Banerjee, G., Scott-Craig, J.S., Walton, J.D., Phillips, G.N.J., Sandgren, M. (2014) Biochemical Characterization and Crystal Structures of a Fungal Family 3 Beta-Glucosidase, Cel3A from Hypocrea Jecorina. J Biol Chem 289: 31624-31637
  5. 4c4c: Knott, B.C., Haddad Momeni, M., Crowley, M.F., Mackenzie, L.F., Gotz, A.W., Sandgren, M., Withers, S.G., Stahlberg, J., Beckham, G.T. (2014) The Mechanism of Cellulose Hydrolysis by a Two-Step, Retaining Cellobiohydrolase Elucidated by Structural and Transition Path Sampling Studies. J Am Chem Soc 136: 321-329
  6. 2vtc: Karkehabadi, S., Hansson, H., Kim, S., Piens, K., Mitchinson, C., Sandgren, M. (2008) The First Structure of a Glycoside Hydrolase Family 61 Member, Cel61B from the Hypocrea Jecorina, at 1.6 A Resolution. J Mol Biol 383: 144-154
  7. 7cel: Divne, C., Stahlberg, J., Teeri, T.T., Jones, T.A. (1998) High-resolution crystal structures reveal how a cellulose chain is bound in the 50 A long tunnel of cellobiohydrolase I from Trichoderma reesei. J Mol Biol 275: 309-325
  8. 1eg1: Kleywegt, G.J., Zou, J.Y., Divne, C., Davies, G.J., Sinning, I., Stahlberg, J., Reinikainen, T., Srisodsuk, M., Teeri, T.T., Jones, T.A. (1997) The crystal structure of the catalytic core domain of endoglucanase I from Trichoderma reesei at 3.6 A resolution, and a comparison with related enzymes. J Mol Biol 272: 383-397

May 2023, David Goodsell

http://doi.org/10.2210/rcsb_pdb/mom_2023_5
About Molecule of the Month
The RCSB PDB Molecule of the Month by David S. Goodsell (The Scripps Research Institute and the RCSB PDB) presents short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details.More