Carbohydrate Esterase Family 1

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• Author: Casper Wilkens
• Responsible Curator: Harry Brumer

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Carbohydrate Esterase Family 1
Fold	α/β/α-sandwich
Mechanism	serine hydrolase
Active site residues	known
CAZy DB link
https://www.cazy.org/CE1.html

Substrate specificities

Carbohydrate esterase family 1 (CE1) is one of the biggest and most diverse CE families, which comprises acetylxylan esterases (EC 3.1.1.72), feruloyl esterases (EC 3.1.1.73), cinnamoyl esterases (EC 3.1.1.-), carboxylesterases (EC 3.1.1.1), S-formylglutathione hydrolases (EC 3.1.2.12), diacylglycerol O-acyltransferases (EC 2.3.1.20), thehalose 6-O-mycolyltransferases (EC 2.3.1.122), and others [1].

Kinetics and Mechanism

CE1 enzymes target a large variety of substrates, however, all appear to utilize the canonical serine hydrolase mechanism, involving a catalytic triad comprising a nucleophilic serine, a histidine, and an acidic amino acid [2, 3]. Both aspartic and glutamic acid are commonly observed in this position [4]. After substrate binding, the serine is activated by the proton relay consisting of the histidine and the acid residue, which facilitates nucleophilic attack on the carbonyl carbon atom of the substrate. This results in the formation of a covalent acyl-enzyme intermediate via a tetrahedral transition state (sometimes known as the "tetrahedral intermediate"), which is stabilized through interactions with two main-chain NH groups in the "oxyanion hole." Following release of the corresponding alcohol as the first product, the acyl-enzyme intermediate is hydrolyzed by the near-microscopic reverse of the first step, with water, activated by the proton relay, acting as the nucleophile [2, 3].

Catalytic Residues

The catalytic serine is located at the center of a conserved pentapeptide with the consensus sequence G-X-S-X-G. This pentapeptide segment constitutes the so-called "nucleophilic elbow", which serves as a fingerprint feature commonly used to identify proteins of this enzyme family based on their primary structure alone [2]. The histidine is also conserved [2, 3], while the general acid may be an aspartic acid or glutamic acid, as introduced above [4].

Three-dimensional structures

The tertiary structure of CE1 members is an α/β/α-sandwich, comprised of a central β-sheet with 8 or 9 strands connected by α-helices [5], placing CE1 within the α/β-hydrolase superfamily [6]. A number of CE1 feruloyl esterases have a CBM48 appended that is essential for feruloyl esterase activity on polymeric xylan in some members [4]. However, there are also examples of CE1 feruloyl esterases lacking a CBM that act on polymeric xylan [7].

Family Firsts

First characterized

Experiments published in a patent application in 1992 showed that an enzyme from Trichoderma reesei later classified as a CE1 enzyme was able to deacetylate xylans [8]. Prior the publication of sequence data in this patent application, the purification and characterization of native fungal acetylxylan esterases was reported [9, 10]. In 2000 more comprehensive characterizations of two CE1 enzymes were published for a cinnamoyl esterase from Penicillium funiculosum [11] and a mycolyltransferase from Mycobacterium tuberculosis [6].

First mechanistic insight

The crystal structure of Mycobacterium tuberculosis H37Rv mycolyltransferase in complex with the covalently bound inhibitor, diethyl phosphate gave the first insight into the mechanism, which involved the highly conserved catalytic Ser-Glu-His triad [6].

First 3-D structure

Mycobacterium tuberculosis H37Rv mycolyltransferase crystal structure in 2000 [6].

References

1. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, and Henrissat B. (2014). The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42(Database issue):D490-5. DOI:10.1093/nar/gkt1178 |
2. Schubot FD, Kataeva IA, Blum DL, Shah AK, Ljungdahl LG, Rose JP, and Wang BC. (2001). Structural basis for the substrate specificity of the feruloyl esterase domain of the cellulosomal xylanase Z from Clostridium thermocellum. Biochemistry. 2001;40(42):12524-32. DOI:10.1021/bi011391c |
3. Prates JA, Tarbouriech N, Charnock SJ, Fontes CM, Ferreira LM, and Davies GJ. (2001). The structure of the feruloyl esterase module of xylanase 10B from Clostridium thermocellum provides insights into substrate recognition. Structure. 2001;9(12):1183-90. DOI:10.1016/s0969-2126(01)00684-0 |
4. Holck J, Fredslund F, Møller MS, Brask J, Krogh KBRM, Lange L, Welner DH, Svensson B, Meyer AS, and Wilkens C. (2019). A carbohydrate-binding family 48 module enables feruloyl esterase action on polymeric arabinoxylan. J Biol Chem. 2019;294(46):17339-17353. DOI:10.1074/jbc.RA119.009523 |
5. Ollis DL, Cheah E, Cygler M, Dijkstra B, Frolow F, Franken SM, Harel M, Remington SJ, Silman I, and Schrag J. (1992). The alpha/beta hydrolase fold. Protein Eng. 1992;5(3):197-211. DOI:10.1093/protein/5.3.197 |
6. Ronning DR, Klabunde T, Besra GS, Vissa VD, Belisle JT, and Sacchettini JC. (2000). Crystal structure of the secreted form of antigen 85C reveals potential targets for mycobacterial drugs and vaccines. Nat Struct Biol. 2000;7(2):141-6. DOI:10.1038/72413 |
7. Wefers D, Cavalcante JJV, Schendel RR, Deveryshetty J, Wang K, Wawrzak Z, Mackie RI, Koropatkin NM, and Cann I. (2017). Biochemical and Structural Analyses of Two Cryptic Esterases in Bacteroides intestinalis and their Synergistic Activities with Cognate Xylanases. J Mol Biol. 2017;429(16):2509-2527. DOI:10.1016/j.jmb.2017.06.017 |

8. L.H. De Graff, et al. (1992) Cloning, expression and use of acetyl xylan esterases from fungal origin. EP0507369A2

9. Poutanen, K., Sundberg, M., Korte, H., Puls, J.(1990) Deacetylation of xylans by acetyl esterases of Trichoderma reesei. Appl Microbiol Biotechnol, 33, 506–510. DOI:10.1007/BF00172542

10. Biely, P., MacKenzie, C.R., Schneider, H. (1988) Production of acetyl xylan esterase by Trichoderma reesei and Schizophyllum commune. Canadian Journal of Microbiology, 34, 767-772. DOI:10.1139/m88-130

11. Kroon PA, Williamson G, Fish NM, Archer DB, and Belshaw NJ. (2000). A modular esterase from Penicillium funiculosum which releases ferulic acid from plant cell walls and binds crystalline cellulose contains a carbohydrate binding module. Eur J Biochem. 2000;267(23):6740-52. DOI:10.1046/j.1432-1033.2000.01742.x |
12. Belisle JT, Vissa VD, Sievert T, Takayama K, Brennan PJ, and Besra GS. (1997). Role of the major antigen of Mycobacterium tuberculosis in cell wall biogenesis. Science. 1997;276(5317):1420-2. DOI:10.1126/science.276.5317.1420 |