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Difference between revisions of "Glycoside Hydrolase Family 57"

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(Catalytic Residues)
(Three-dimensional structures)
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== Three-dimensional structures ==
 
== Three-dimensional structures ==
 
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    Normal  0        21        false  false  false      SK  X-NONE  X-NONE                                                    MicrosoftInternetExplorer4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    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 (Fig. 2) that, in the case of the T. litoralis 4-α-glucanotransferase (Imamura et al. 2003) is succeeded by the C-terminal non-catalytic domain consisting of β-strands only adopting a twisted β-sandwich fold (Fig. 2). In the three-dimensional structure of the α-amylase AmyC from Thermotoga maritima (Dickmanns et al. 2006; PDB: 2b5d), the corresponding catalytic (β/α)7-barrel is followed by a five-helix domain C and a small helical domain B protruding 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 (Imamura et al. 2003, Dickmanns et al. 2006). There was also a crystallization report in 1995 on a probable GH57 amylopullulanase from Pyrococcus woesei (Knapp et al. 1995), but the detailed crystallographic analysis of this protein has not been published as yet.
  
 
== Family Firsts ==
 
== Family Firsts ==

Revision as of 02:41, 13 January 2010

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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 (Henrissat & Bairoch 1996) based on the existence of the sequences of two “α-amylases” that were dissimilar to typical family GH13 α-amylases (MacGregor et al. 2001). The two were the heat-stable eubacterial amylase from Dictyoglomus thermophilum known from 1988 (Fukusumi et al. 1988) and the extremely thermostable archaeal amylase from Pyrococcus furiosus determined in 1993 (Laderman et al. 1993a).

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 (Nakajima et al. 2004), whereas the latter was shown already in 1993 to exhibit the 4-α-glucanotransferase activity (Laderman et al., 1993b). 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

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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 (Janecek 2005). 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 (Fig. 1) were identified and proposed by Zona et al. (2004). This was possible to achieve since the catalytic nucleophile (Glu123) in the GH57 4-α-glucanotransferase from Thermococcus litoralis (Imamura et al. 2001) was known together with its three-dimensional structure (Imamura et al. 2003; PDB: 1k1w) that revealed also the proton donor (Asp214). Thus the first catalytic machinery and the first three-dimensional structure for a GH57 member (Fig. 2) were those of the archaeal 4-α-glucanotransferase from T. litoralis (Imamura et al. 2001, 2003).

The catalytic nucleophile (a glutamate) and proton donor (an aspartate) are located in the conserved sequence regions 3 and 4, respectively (Fig. 1). In addition to T. litoralis 4-α-glucanotransferase, they were identified also in the amylopullulanases from Thermococcus hydrothermalis (Zona et al. 2004) and P. furiosus (Kang et al. 2005). The catalytic nucleophile was confirmed also in the α-galactosidase from P. furiosus although without success to find the catalytic proton donor (van Lieshout et al. 2003). 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 (Zona et al. 2004).

Based on the five identified conserved sequence regions (Fig. 1), the residues His13, Glu79, Glu216, Asp354 together with the Trp120, Trp221 and Trp357 (T. hydrothermalis 4-α-glucanotransferase numbering) were postulated (Zona et al. 2004) as eventually important for the individual GH57 enzyme specificities (Fig. 3). 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 P. furiosus exhibited markedly decreased transglycosylation activity in comparison with the wild-type counterpart (Tang et al. 2006).

Three-dimensional structures

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    Normal   0         21         false   false   false      SK   X-NONE   X-NONE                                                     MicrosoftInternetExplorer4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     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 (Fig. 2) that, in the case of the T. litoralis 4-α-glucanotransferase (Imamura et al. 2003) is succeeded by the C-terminal non-catalytic domain consisting of β-strands only adopting a twisted β-sandwich fold (Fig. 2). In the three-dimensional structure of the α-amylase AmyC from Thermotoga maritima (Dickmanns et al. 2006; PDB: 2b5d), the corresponding catalytic (β/α)7-barrel is followed by a five-helix domain C and a small helical domain B protruding 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 (Imamura et al. 2003, Dickmanns et al. 2006). There was also a crystallization report in 1995 on a probable GH57 amylopullulanase from Pyrococcus woesei (Knapp et al. 1995), but the detailed crystallographic analysis of this protein has not been published as yet.

Family Firsts

First sterochemistry determination
Cite some reference here, with a short (1-2 sentence) explanation.
First catalytic nucleophile identification
Cite some reference here, with a short (1-2 sentence) explanation.
First general acid/base residue identification
Cite some reference here, with a short (1-2 sentence) explanation.
First 3-D structure
The first 3-D structure of a GH57 member was that of the 4-alpha-glucanotransferase from Thermococcus litoralis [1].

References

  1. 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. 278, 19378-86. DOI:10.1074/jbc.M213134200 | PubMed ID:12618437 | HubMed [Imamura2003]