Glycoside Hydrolase Family 9

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• Author: ^^^David Wilson^^^
• Responsible Curator: ^^^David Wilson^^^

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Glycoside Hydrolase Family GH9
Clan	GH-G
Mechanism inverting
Active site residues	known/known
CAZy DB link
http://www.cazy.org/fam/GHnn.html

Substrate specificities

Content is to be added here. GH Family 9 is an inverting glycohydrolase family that mainly contains cellulases and is the second largest cellulase family. It contains mainly endoglucanases with a few processive endoglucanases. All of the processive endoglucanases contain a family 3c CBM rigidly attached to the C-terminus of the family 9 catalytic domain (cd). This domain is part of the active site and is essential for processivity (1) CBM3c domains bind weakly to cellulose as they lack several of the conserved aromatic residues that are important for cellulose binding in family 3a and family 3b members (2). All known plant cellulases belong to family 9, and most of the other members are eubacterial although there are two archael members and some fungal, earthworm, arthropod, chordate, echinoderma and molusk members (http://www.cazy.org/fam/acc_GH.html). There are two subgroups in family 9, E1 which contains only cellulases from bacteria, including ones from both aerobes and anaeobes, and E2 which includes some bacterial and all nonbacterial cellulases (3). An evolutionary study shows that the eucaryote members contain two monophyletic groups that are amcient; one including all anamal members and the other including all plant members (4). All known processive endoglucanase genes are in subgroup E1.

This is an example of how to make references to a journal article [1]. (See the References section below). Multiple references can go in the same place like this [1, 2]. You can even cite books using just the ISBN [3]. References that are not in PubMed can be typed in by hand [4].

Kinetics and Mechanism

Content is to be added here. The processive endoglucanase,Cel9A from Thermobifda fusca, has high activity on bacterial cellulose and is the only cellulase tested that can degrade crystalline regions in bacterial cellulose by itself although it prefers amorphous regions (7). A related cellulase in Clostridium phytofermentans, which is the only family 9 cellulase encoded in its genome, has been shown to be essential for cellulose degradation by this organism. This is the only case where a single cellulase has been shown to be essential for growth on cellulose (8).

Catalytic Residues

Content is to be added here. There is a conserved Glu residue that functions as the catalytic acid and two conserved Asp residues that bind the catalytic water, with one functioning as the catalytic base and mutation of the other also greatly reduces activity on all substrates (6).

Three-dimensional structures

Content is to be added here. All known family 9 cd structures have an ( a / a ) 6 barrel fold that contains an open active site cleft that contains at least six sugar binding subsites -4 to +2 (1,5).

Family Firsts

First sterochemistry determination

Cite some reference here, with a short (1-2 sentence) explanation [1].

PMID: 1618761 J Gebler, N R Gilkes, M Claeyssens, D B Wilson, P Béguin, W W Wakarchuk, D G Kilburn, R C Miller, Jr, R A Warren, and S G Withers. Stereoselective hydrolysis catalyzed by related beta-1,4-glucanases and beta-1,4-xylanases. J. Biol. Chem. 1992 267: 12559-12561. The steriospecificity of three family 9 cellulases were all determined to be inverting by NMR.

First catalytic nucleophile identification

Cite some reference here, with a short (1-2 sentence) explanation [4].

First general acid/base residue identification

Cite some reference here, with a short (1-2 sentence) explanation [2].

First 3-D structure

Cite some reference here, with a short (1-2 sentence) explanation [3].1CLC[A] Lascombe, M.B., Souchon, H., Juy, M., Alzari, P.M. Three-Dimensional Structure of Endoglucanase D at 1.9 Angstroms Resolution. Unpuplished.The structure of endocellulase CelD from C. thermocellum was determined by X-ray crystallography.

References

1. Comfort DA, Bobrov KS, Ivanen DR, Shabalin KA, Harris JM, Kulminskaya AA, Brumer H, and Kelly RM. (2007). Biochemical analysis of Thermotoga maritima GH36 alpha-galactosidase (TmGalA) confirms the mechanistic commonality of clan GH-D glycoside hydrolases. Biochemistry. 2007;46(11):3319-30. DOI:10.1021/bi061521n |
2. He S and Withers SG. (1997). Assignment of sweet almond beta-glucosidase as a family 1 glycosidase and identification of its active site nucleophile. J Biol Chem. 1997;272(40):24864-7. DOI:10.1074/jbc.272.40.24864 |
3. Robert V. Stick and Spencer J. Williams. (2009) Carbohydrates. Elsevier Science.

4. Sinnott, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202. DOI: 10.1021/cr00105a006

5. . Sakon, J., Irwin, D., Wilson, D.B. and Karplus, P.A. Structure and mechanism of endo/exocellulase E4 from Thermomonospora fusca. Nature Structural Biology 1997: 4, 810-818. PMID: 9334746

   2. Tormo, J, Tormo, R Lamed, A J Chirino, E Morag, E A Bayer, Y Shoham, and T A Steitz

   Crystal structure of a bacterial family-III cellulose-binding domain: a general mechanism for attachment to cellulose. EMBO J. 1996; 15: 5739–5751. PMID: 8918451

   3. Tomme P., R. A. J. Warren, and N. R. Gilkes.. Cellulose hydrolysis by bacteria and fungi. Adv. Microb. Physiol. 1995: 37:1–81. PMID: 8540419

   4. Davison A, Blaxter M. Ancient origin of glycosyl hydrolase family 9 cellulase genes. Mol Biol Evol. 2005 ;22:1273-84. PMID: 15703240

   5. Guérin DM, Lascombe MB, Costabel M, Souchon H, Lamzin V, Béguin P, Alzari PM.Atomic (0.94 A) resolution structure of an inverting glycosidase in complex with substrate. J Mol Biol. 2002 ;316:1061-9. PMID: 11884144

   6. Zhou, W., Irwin, D.C., Escovar-Kousen, J. and Wilson, D.B. Kinetic studies of Thermobifida fusca Cel9A active site mutant enzymes. Biochem. 43, 9655-9663 (2004). PMID: 15274620

   Li Y, Irwin DC, Wilson DB. Processivity, substrate binding, and mechanism of

   cellulose hydrolysis by Thermobifida fusca Cel9A. Appl Environ Microbiol. 2007;73:3165-72. PMID: 17369336

   7. Yao Chen, Arthur J. Stipanovic, William T. Winter, David B. Wilson and Young-Jun Kim. Effect of digestion by pure cellulases on crystallinity and average chain length for bacterial and microcrystalline celluloses. Cellulose 2007: 14: 283-293.

   8. Tolonen AC, Chilaka AC, Church GM. Targeted gene inactivation in Clostridium phytofermentans shows that cellulose degradation requires the family 9 hydrolase Cphy3367. Mol Microbiol. 2009 ;74:1300-13. PMID: 19775243