Molecule of the Month: Cellulases and Bioenergy
Powerful fungal enzymes break down cellulose during industrial production of ethanol from plant material.
Science of Cellulases
Exploring the Structure
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
- You can find many other structures of cellulases by using the EC number in the Annotation Browser for 220.127.116.11 (cellulases) and 18.104.22.168 (cellulose 1,4-beta-cellobiosidases).
- 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.
- 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
- Browse Biological Energy
- Browse Renewable Energy
- Robak, K., Balcerek, M. (2020) Current state-of-the-art in ethanol production from lignocellulosic feedstocks. Microbiol Res 240: 126534
- 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
- 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
- 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
- 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
- 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
- 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
- 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 Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2023_5