Glycoside Hydrolase Family 57

This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.

• Author: ^^^Stefan Janecek^^^
• Responsible Curator: ^^^Stefan Janecek^^^

---

Glycoside Hydrolase Family GH57
Clan	not assigned yet
Mechanism	retaining
Active site residues	known/not known
CAZy DB link
http://www.cazy.org/fam/GH57.html

Substrate specificities

The family GH57 was established in 1996 [1] based on the existence of the sequences of two “α-amylases” that were dissimilar to typical family GH13 α-amylases [2]. The two were the heat-stable eubacterial amylase from Dictyoglomus thermophilum known from 1988 [3] and the extremely thermostable archaeal amylase from Pyrococcus furiosus determined in 1993 [4].

The family has expanded mainly due to running genome sequencing projects. Nowadays it contains more than 400 members; all originating from prokaryotes (http://www.cazy.org/fam/GH57.html). With regard to the enzyme specificities, the family GH57 covers the α-amylase (EC 3.2.1.1), α-galactosidase (EC 3.2.1.22), amylopullulanase (EC 3.2.1.1/41), branching enzyme (EC 2.4.1.18) and 4-α-glucanotransferase (EC 2.4.1.25). It is worth mentioning that the two constituent members, i.e. the “α-amylases” from D. thermophilum and P. furiosus are rather the 4-α-glucanotransferases since the former was later proven to have the transglycosylating activity [5], whereas the latter was shown already in 1993 to exhibit the 4-α-glucanotransferase activity [6]. And it is also of interest that the real enzymes form only about 5% of the family members. The vast majority of the GH57 are hypothetical proteins.

Kinetics and Mechanism

Family GH57 are retaining enzymes, as first documented by the X-ray crystallography on the 4-α-glucanotransferase from Thermococcus litoralis complexed with acarbose [7]. Kinetic studies have been performed with the 4-α-glucanotransferases from Thermococcus litoralis [7, 8], Pyrococcus furiosus [9], amylopullulanases from Thermococcus hydrothermalis [10] and Pyrococcus furiosus [11] and branching enzyme from Thermococcus kodakaraensis [12].

Catalytic Residues

In addition, the sequences of GH57 members are extremely diversified. Certain sequences are shorter than 400 residues whereas others are longer than 1,500 residues [13]. This complicated the previous efforts to align the GH57 sequences using the routine alignment programs. Based on a detailed bioinformatics study focused on all available GH57 sequences at that time, five conserved sequence regions in the family GH57 were identified and proposed by [10]. This was possible to achieve since the catalytic nucleophile (Glu123) in the GH57 4-α-glucanotransferase from Thermococcus litoralis [8] was known together with its three-dimensional structure [7] (PDB: 1k1w) that revealed also the proton donor (Asp214).

The catalytic nucleophile (a glutamate) and proton donor (an aspartate) are located in the conserved sequence regions 3 and 4, respectively. In addition to Thermococcus litoralis 4-α-glucanotransferase, they were identified also in the amylopullulanases from Thermococcus hydrothermalis [10] and Pyrococcus furiosus [11]. The catalytic nucleophile was confirmed also in the α-galactosidase from Pyrococcus furiosus although without success to find the catalytic proton donor [14]. It should be taken into account, however, that some GH57 members, which are only hypothetical enzymes/proteins without any biochemical characterization, may lack one or even both catalytic residues [10].

Based on the five identified conserved sequence regions, the residues His13, Glu79, Glu216, Asp354 together with the Trp120, Trp221 and Trp357 (Thermococcus hydrothermalis 4-α-glucanotransferase numbering) were postulated [10] as eventually important for the individual GH57 enzyme specificities. Of these, the Trp221 has already been confirmed to contribute to the transglycosylation activity of 4-α-glucanotransferase since the mutant W229H of the enzyme from Pyrococcus furiosus exhibited markedly decreased transglycosylation activity in comparison with the wild-type counterpart [9].

Three-dimensional structures

The structure of the catalytic domain adopts a (β/α)7-barrel, i.e. the irregular (β/α)8-barrel called also a pseudo TIM-barrel that, in the case of the Thermococcus litoralis 4-α-glucanotransferase [7] is succeeded by the C-terminal non-catalytic domain consisting of β-strands only adopting a twisted β-sandwich fold. In the three-dimensional structure of the α-amylase AmyC from Thermotoga maritima [15] (PDB: 2b5d), the corresponding catalytic (β/α)7-barrel is followed by a five-helix domain C, a small helical domain B being protruded out of the catalytic pseudo TIM barrel in the place of the loop 2 (i.e. succeeding the strand β2). This structure was found to be most closely similar to that of the GH57 member of unknown function from Thermus thermophilus (PDB: 1ufa). In all cases, the catalytic glutamic acid and aspartic acid residues are located near the C-terminal ends of the strands β4 and β7 of the barrel, respectively [7, 15]. There was also a crystallization report in 1995 on a probable GH57 amylopullulanase from Pyrococcus woesei [16], but the detailed crystallographic analysis of this protein has not been published as yet.

It is clear that the C-terminal domain cannot be present in some GH57 members with shorter amino acid sequences, e.g., in the α-galactosidases containing less than 400 residues [14]. On the other hand, some other GH57 members, especially the extra-long amylopullulanases with more than 1,300 residues [17] have to contain even additional domains. One of them is a longer version of a typical SLH motif (surface layer homology) [18] that was named as the so-called SLH motif-bearing domain in the amylopullulanase from Thermococcus hydrothermalis [17]. This domain was found also in the GH15 glucodextranase from Arthrobacter globiformis [19]. Remarkably, within the family GH57, the presence of this SLH motif-bearing domain is restricted only for amylopullulanases [20].

It is also worth mentioning that, especially prior the first three-dimensional structure of a GH57 member was available, there were some efforts to join the family GH57 with the main α-amylase family GH13, i.e. the present clan GH-H consisting of the families GH13, GH70 and GH77 [2]. Those efforts were focused mainly on looking for some remote homology at the sequence level only [21, 22]. Although both GH57 and GH-H employ the same retaining reaction mechanism [7, 23] the independence of the family GH57 with regard to GH-H clan is at present based not only on differences in the catalytic domain, but more importantly, due to differences in the catalytic machineries and conserved sequence regions [10, 24]. As far as other GH families are concerned, the family GH38 α-mannosidase from Drosophila melanogaster [25] was revealed to share some structural similarities within the catalytic domain with the GH57 4-α-glucanotransferase from Thermococcus litoralis [7, 8] indicating an eventuality of originating from a common ancestor.

Family Firsts

First sterochemistry determination

Probably the work on the 4-α-glucanotransferase from Thermococcus litoralis [7] or that on branching enzyme from Thermococcus kodakaraensis [12].

First amino acid sequence determination

The first amino acid sequence of the family GH57 was that of a heat stable amylase from an anaerobic thermophilic bacterium Dictyoglomus thermophilum [3]. This "α-amylase" was later characterized as 4-α-glucanotransferase [5].

First conserved sequence regions determination

The five sequence stretches characteristic as conserved regions for the family GH57 were first determined by the bioinformatics study by [10].

First catalytic nucleophile identification

The catalytic nucleophile was fist identified by [8] as Glu123 in the 4-α-glucanotransferase from Thermococcus litoralis using the 3-ketobutylidene-β-2-chloro-4-nitrophenyl maltopentaoside as a donor.

First general acid/base residue identification

Asp214 of the 4-α-glucanotransferase from Thermococcus litoralis as indicated by the X-ray crystallography and supported by site-directed mutagenesis [7] since the D214N mutant exhibited a 10,000-fold decrease of specific activity in comparison with the wild-type enzyme).

First 3-D structure

The first 3-D structure of a GH57 member was that of the 4-α-glucanotransferase from Thermococcus litoralis [7].

References

1. Henrissat B and Bairoch A. (1996). Updating the sequence-based classification of glycosyl hydrolases. Biochem J. 1996;316 ( Pt 2)(Pt 2):695-6. DOI:10.1042/bj3160695 |
2. Janecek S, Svensson B, and MacGregor EA. (2003). Relation between domain evolution, specificity, and taxonomy of the alpha-amylase family members containing a C-terminal starch-binding domain. Eur J Biochem. 2003;270(4):635-45. DOI:10.1046/j.1432-1033.2003.03404.x |
7. Imamura H, Fushinobu S, Yamamoto M, Kumasaka T, Jeon BS, Wakagi T, and Matsuzawa H. (2003). Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor. J Biol Chem. 2003;278(21):19378-86. DOI:10.1074/jbc.M213134200 |

8. pmid=

12. Murakami T, Kanai T, Takata H, Kuriki T, and Imanaka T. (2006). A novel branching enzyme of the GH-57 family in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J Bacteriol. 2006;188(16):5915-24. DOI:10.1128/JB.00390-06 |
22. Janecek S (1998). Sequence of archaeal Methanococcus jannaschii alpha-amylase contains features of families 13 and 57 of glycosyl hydrolases: a trace of their common ancestor?. Folia Microbiol (Praha). 1998;43(2):123-8. DOI:10.1007/BF02816496 |

26. , S., Kamizono, A., Horinouchi, S. & Beppu, T. 1988. Eur. J. Biochem. 174: 15-21.

27. , K.A., Asada, K., Uemori, T., Mukai, H., Taguchi, Y., Kato, I. & Anfinsen, C.B. 1993a. J. Biol. Chem. 268: 24402-24407.

27. , K.A., Davis, B.R., Krutzsch, H.C., Lewis, M.S., Griko. Y.V., Privalov, P.L. & Anfinsen, C.B. 1993b. J. Biol. Chem. 268: 24394-24401.

28. , M., Imamura, H., Shoun, H., Horinouchi, S. & Wakagi, T. 2004. Biosci. Biotechnol. Biochem. 68: 2369-2373.

29. SY, Yang SJ, Cha H, Woo EJ, Park C, Park KH. Contribution of W229 to the transglycosylation activity of 4-alpha-glucanotransferase from Pyrococcus furiosus. Biochim Biophys Acta. 2006 Oct;1764(10):1633-8. Epub 2006 Sep 1.

30. , R. & Janecek, S. 2005. Biologia 60 (Suppl. 16): 115-121.

30. , R., Chang-Pi-Hin, F., O’Donohue, M.J. & Janecek, S. 2004. Eur. J. Biochem. 271: 2863-2872.

31. , S., Vieille, C. & Zeikus, J.G. 2005. Appl. Microbiol. Biotechnol. 66: 408-413.

32. , S. 2002. Biologia, Bratislava 57 (Suppl. 11): 29-41.

32. , S. 2005. Biologia 60 (Suppl. 16): 177-184.

33. Lieshout, J.F.T., Verhees, C.H., Ettema, T.J.G., van der Saar, S., Imamura, H., Matsuzawa, H.,

33. den Elsen, J.M.H., Kuntz, D.A. & Rose, D.R. 2001. EMBO J. 20: 3008-3017.

34. A, Ballschmiter M, Liebl W, Ficner R. Structure of the novel alpha-amylase AmyC from Thermotoga maritima. Acta Crystallogr D Biol Crystallogr. 2006 Mar;62(Pt 3):262-70. Epub 2006 Feb 22.

35. , S., Rudiger, A., Antranikian, G., Jorgensen, P.L. & Ladenstein, R. 1995. Proteins 23: 595-597.

36. , M., Debeire, P., Duchiron, F. & O’Donohue, M.J. 1999. J. Bacteriol. 181: 3284-3287.

37. , A., ENGELHARDT, H., PETERS, J., SANTARIUS, U., VOLKER, S. & BAUMEISTER, W. 1994. Domain structure of the Acetogenium kivui surface layer revealed by electron crystallography and sequence analysis. J. Bacteriol. 176: 1224–1233.

38. , M., Tonozuka, T., Suzuki, S., Uotsu-Tomita, R., Kamitori, S., Nishikawa, A. & Sakano, Y. 2004. J. Biol. Chem. 279: 10575-10583.

39. , G., Vieille, C. & Zeikus, J.G. 1997. Appl. Environ. Microbiol. 63: 3577-3584.

40. , Y., Kusunoki, M., Harada, W. & Kakudo, M. 1984. J. Biochem. 95: 697-702.