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Difference between revisions of "Glycoside Hydrolase Family 36"
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== Kinetics and Mechanism == | == Kinetics and Mechanism == | ||
| − | Family GH36 alpha-galactosidases are retaining enzymes, as first shown by NMR <cite>1</cite> and | + | Family GH36 alpha-galactosidases are anomeric configuration-retaining enzymes, like their [[Glycoside Hydrolase Family 36 (GH36)|Family GH27]] relatives in Clan GH-D, as first shown by NMR <cite>1</cite>. In addition to NMR data, mutagenesis and azide rescue experiments in this study <cite>1</cite> established that Clan GH-D enzymes in both GH27 and GH36 use a classical Koshland double-displacement mechanism. Enzymes that have been well-studied kinetically include the ''Cellulomonas fimi'' endo-glycanase (Cex)'''*''', for which a detailed kinetic study involving both steady state and pre-steady state kinetic analyses was performed <cite>2</cite>. Recent studies of the roles of each substrate hydroxyl in catalysis have also been described <cite>3</cite>. Detailed analyses of substrate and subsite specificities of the ''Pseudomonas cellulosa'' xylanase have also been described <cite>4</cite>. |
== Catalytic Residues == | == Catalytic Residues == | ||
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== Three-dimensional structures == | == Three-dimensional structures == | ||
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== Family Firsts == | == Family Firsts == | ||
;First sterochemistry determination: ''Thermotoga maritima'' alpha-galactosidase, by NMR <cite>1</cite>. | ;First sterochemistry determination: ''Thermotoga maritima'' alpha-galactosidase, by NMR <cite>1</cite>. | ||
| − | ;First catalytic nucleophile identification: ''Thermotoga maritima'' alpha-galactosidase | + | ;First catalytic nucleophile identification: ''Sulfolobus solfataricus'' alpha-galactosidase GalS, by sequence homology with GH27 enzymes and mutagenesis <cite>3</cite>. Subsequently confirmed in ''Thermotoga maritima'' alpha-galactosidase by structural homology, mutagenesis, and azide rescue <cite>1</cite>. |
| − | ;First general acid/base residue identification: ''Thermotoga maritima'' alpha-galactosidase | + | ;First general acid/base residue identification: ''Sulfolobus solfataricus'' alpha-galactosidase GalS, by sequence homology with GH27 enzymes and mutagenesis <cite>3</cite>. Subsequently confirmed in ''Thermotoga maritima'' alpha-galactosidase by structural homology, mutagenesis, and azide rescue <cite>1</cite>. |
| − | ;First 3-D structure: ''Thermotoga maritima'' alpha-galactosidase. Coordinates first reported as part of a high-throughput functional genomics project <cite>2</cite>, structural | + | ;First 3-D structure: ''Thermotoga maritima'' alpha-galactosidase. Coordinates first reported as part of a high-throughput functional genomics project <cite>2</cite>, structural analysis reported in ref. <cite>1</cite>. |
== References == | == References == | ||
<biblio> | <biblio> | ||
#1 pmid=17323919 | #1 pmid=17323919 | ||
| − | #2 pmid= | + | #2 pmid=12193646 |
| − | #3 pmid= | + | #3 pmid=16547025 |
| − | #4 | + | #4 Sinnott, M.L. (1990) Catalytic mechanisms of enzymatic glycosyl transfer. Chem. Rev. 90, 1171-1202. [http://dx.doi.org/10.1021/cr00105a006 DOI: 10.1021/cr00105a006] |
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</biblio> | </biblio> | ||
[[Category:Glycoside Hydrolase Families]] | [[Category:Glycoside Hydrolase Families]] | ||
Revision as of 12:03, 27 May 2007
| Glycoside Hydrolase Family GH36 | |
| Clan | GH-D |
| Mechanism | retaining |
| Active site residues | known |
| CAZy DB link | |
| http://www.cazy.org/fam/GH36.html | |
Substrate specificities
Alpha-galactosidase and alpha-N-acetylgalactosaminidase activity has been demonstrated in archaeal, bacterial, and eukaryotic members of this family. Additionally, certain plant members of this family possess stachyose synthase or raffinose synthase activity.
Kinetics and Mechanism
Family GH36 alpha-galactosidases are anomeric configuration-retaining enzymes, like their Family GH27 relatives in Clan GH-D, as first shown by NMR [1]. In addition to NMR data, mutagenesis and azide rescue experiments in this study [1] established that Clan GH-D enzymes in both GH27 and GH36 use a classical Koshland double-displacement mechanism. Enzymes that have been well-studied kinetically include the Cellulomonas fimi endo-glycanase (Cex)*, for which a detailed kinetic study involving both steady state and pre-steady state kinetic analyses was performed [2]. Recent studies of the roles of each substrate hydroxyl in catalysis have also been described [3]. Detailed analyses of substrate and subsite specificities of the Pseudomonas cellulosa xylanase have also been described [4].
Catalytic Residues
Three-dimensional structures
Family Firsts
- First sterochemistry determination
- Thermotoga maritima alpha-galactosidase, by NMR [1].
- First catalytic nucleophile identification
- Sulfolobus solfataricus alpha-galactosidase GalS, by sequence homology with GH27 enzymes and mutagenesis [3]. Subsequently confirmed in Thermotoga maritima alpha-galactosidase by structural homology, mutagenesis, and azide rescue [1].
- First general acid/base residue identification
- Sulfolobus solfataricus alpha-galactosidase GalS, by sequence homology with GH27 enzymes and mutagenesis [3]. Subsequently confirmed in Thermotoga maritima alpha-galactosidase by structural homology, mutagenesis, and azide rescue [1].
- First 3-D structure
- Thermotoga maritima alpha-galactosidase. Coordinates first reported as part of a high-throughput functional genomics project [2], structural analysis reported in ref. [1].
References
- 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 |
- Lesley SA, Kuhn P, Godzik A, Deacon AM, Mathews I, Kreusch A, Spraggon G, Klock HE, McMullan D, Shin T, Vincent J, Robb A, Brinen LS, Miller MD, McPhillips TM, Miller MA, Scheibe D, Canaves JM, Guda C, Jaroszewski L, Selby TL, Elsliger MA, Wooley J, Taylor SS, Hodgson KO, Wilson IA, Schultz PG, and Stevens RC. (2002). Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc Natl Acad Sci U S A. 2002;99(18):11664-9. DOI:10.1073/pnas.142413399 |
- Brouns SJ, Smits N, Wu H, Snijders AP, Wright PC, de Vos WM, and van der Oost J. (2006). Identification of a novel alpha-galactosidase from the hyperthermophilic archaeon Sulfolobus solfataricus. J Bacteriol. 2006;188(7):2392-9. DOI:10.1128/JB.188.7.2392-2399.2006 |
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Sinnott, M.L. (1990) Catalytic mechanisms of enzymatic glycosyl transfer. Chem. Rev. 90, 1171-1202. DOI: 10.1021/cr00105a006