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CATH domain | Related DB codes (homologues) |
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3.20.20.80 : TIM Barrel | S00202,S00210,S00748,S00906,S00907,S00911,S00912,S00915,M00134,M00160,D00479,S00204,S00205,S00206,S00207,S00203,S00208,S00209,S00211,S00213,S00214,M00113,T00307,D00165,D00166,D00169,D00176,D00501,D00502,D00503,D00861,D00864,M00026,M00112,M00193,M00346,T00057,T00062,T00063,T00066,T00067 |
Enzyme Name | UniProtKB | KEGG |
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| P36906 | Q9ZFM2 |
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Protein name | Beta-xylosidase | Beta-xylosidase | Xylan 1,4-beta-xylosidaseXylobiaseBeta-xylosidaseExo-1,4-beta-xylosidaseBeta-D-xylopyranosidaseBeta-xylosidaseBeta-xylosidaseExo-1,4-xylosidaseExo-1,4-beta-D-xylosidase1,4-beta-D-xylan xylohydrolase |
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Synonyms | EC 3.2.1.371,4-beta-D-xylan xylohydrolaseXylan 1,4-beta-xylosidase | EC 3.2.1.371,4-beta-D-xylan xylohydrolaseXylan 1,4-beta-xylosidase |
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Pfam | PF01229 (Glyco_hydro_39) [Graphical view]
| PF01229 (Glyco_hydro_39) [Graphical view]
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CAZy | GH39 (Glycoside Hydrolase Family)
| GH39 (Glycoside Hydrolase Family)
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KEGG pathways | MAP code | Pathways |
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MAP00500 | Starch and sucrose metabolism | MAP00520 | Nucleotide sugars metabolism |
UniProtKB:Accession Number | P36906 | Q9ZFM2 |
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Entry name | XYNB_THESA | XYNB_BACST |
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Activity | Hydrolysis of 1,4-beta-D-xylans, to remove successive D-xylose residues from the non-reducing termini. | Hydrolysis of 1,4-beta-D-xylans, to remove successive D-xylose residues from the non-reducing termini. |
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Subunit |
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Subcellular location |
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Cofactor |
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Compound table: links to PDB-related databases & PoSSuM |
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| Substrates | Products | intermediates |
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KEGG-id | L00052 | C02352 | C02337 | C00001 | L00052 | C02352 | C02337 | C02096 | I00061 |
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Compound | Xylan | 1,4-beta-D-Xylan | beta-D-Xyloside | H2O | Xylan | 1,4-beta-D-Xylan | beta-D-Xyloside | beta-D-Xylose | Peptidyl-Glu-D-xylose |
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Type | aromatic ring (only carbon atom),carboxyl group,polysaccharide | polysaccharide | polysaccharide | H2O | aromatic ring (only carbon atom),carboxyl group,polysaccharide | polysaccharide | polysaccharide | carbohydrate |
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ChEBI |
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| 15377
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| 28161
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PubChem |
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| 22247451 962
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| 125409
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| | | | | | | | | | | | | | | | |
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1px8A01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1px8B01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1uhvA01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1uhvB01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1uhvC01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1uhvD01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1w91A01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1w91B01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1w91C01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1w91D01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1w91E01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1w91F01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1w91G01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1w91H01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bfgA01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bfgB01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bfgC01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bfgD01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bfgE01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bfgF01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bfgG01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bfgH01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bs9A01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bs9B01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bs9C01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bs9D01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bs9E01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bs9F01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bs9G01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bs9H01 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1px8A02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Bound:XYP | Unbound |
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1px8B02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Bound:XYP | Unbound |
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1uhvA02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Intermediate-analogue:DFX |
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1uhvB02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Intermediate-analogue:DFX |
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1uhvC02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Intermediate-analogue:DFX |
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1uhvD02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Intermediate-analogue:DFX |
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1w91A02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1w91B02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1w91C02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1w91D02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1w91E02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1w91F02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1w91G02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1w91H02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bfgA02 |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:ANX-XYP | | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:XYS |
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2bfgB02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:XYS |
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2bfgC02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:XYS |
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2bfgD02 |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:ANX-XYP | | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:XYS |
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2bfgE02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:XYS |
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2bfgF02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:XYS |
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2bfgG02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:XYS |
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2bfgH02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:XYS |
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2bs9A02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bs9B02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bs9C02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bs9D02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bs9E02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bs9F02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bs9G02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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2bs9H02 |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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References for Catalytic Mechanism | References | Sections | No. of steps in catalysis |
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[5] | Scheme 1 |
| [6] | Figure 5, p.159-162 |
| [7] | Figure 4, p.841-844 |
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references | [1] |
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Comments | CHARACTERIZATION. |
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PubMed ID | 8612648 |
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Journal | Eur J Biochem |
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Year | 1996 |
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Volume | 236 |
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Pages | 706-13 |
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Authors | Armand S, Vieille C, Gey C, Heyraud A, Zeikus JG, Henrissat B |
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Title | Stereochemical course and reaction products of the action of beta-xylosidase from Thermoanaerobacterium saccharolyticum strain B6A-RI. |
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[2] |
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Comments | ACTIVE SITE GLU-277, MASS SPECTROMETRY. |
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PubMed ID | 9761746 |
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Journal | Biochem J |
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Year | 1998 |
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Volume | 335 |
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Pages | 449-55 |
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Authors | Vocadlo DJ, MacKenzie LF, He S, Zeikus GJ, Withers SG |
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Title | Identification of glu-277 as the catalytic nucleophile of Thermoanaerobacterium saccharolyticum beta-xylosidase using electrospray MS. |
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[3] |
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PubMed ID | 11322958 |
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Journal | FEBS Lett |
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Year | 2001 |
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Volume | 495 |
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Pages | 115-9 |
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Authors | Bravman T, Mechaly A, Shulami S, Belakhov V, Baasov T, Shoham G, Shoham Y |
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Title | Glutamic acid 160 is the acid-base catalyst of beta-xylosidase from Bacillus stearothermophilus T-6: a family 39 glycoside hydrolase. |
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[4] |
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PubMed ID | 12146939 |
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Journal | Biochemistry |
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Year | 2002 |
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Volume | 41 |
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Pages | 9736-46 |
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Authors | Vocadlo DJ, Wicki J, Rupitz K, Withers SG |
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Title | A case for reverse protonation: identification of Glu160 as an acid/base catalyst in Thermoanaerobacterium saccharolyticum beta-xylosidase and detailed kinetic analysis of a site-directed mutant. |
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[5] |
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PubMed ID | 12146938 |
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Journal | Biochemistry |
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Year | 2002 |
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Volume | 41 |
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Pages | 9727-35 |
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Authors | Vocadlo DJ, Wicki J, Rupitz K, Withers SG |
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Title | Mechanism of Thermoanaerobacterium saccharolyticum beta-xylosidase: kinetic studies. |
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[6] |
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Comments | X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) |
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PubMed ID | 14659747 |
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Journal | J Mol Biol |
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Year | 2004 |
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Volume | 335 |
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Pages | 155-65 |
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Authors | Yang JK, Yoon HJ, Ahn HJ, Lee BI, Pedelacq JD, Liong EC, Berendzen J, Laivenieks M, Vieille C, Zeikus GJ, Vocadlo DJ, Withers SG, Suh SW |
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Title | Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase. |
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Related PDB | 1px8,1uhv |
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Related UniProtKB | P36906 |
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[7] |
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Comments | X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) |
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PubMed ID | 16212978 |
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Journal | J Mol Biol |
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Year | 2005 |
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Volume | 353 |
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Pages | 838-46 |
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Authors | Czjzek M, Ben David A, Bravman T, Shoham G, Henrissat B, Shoham Y |
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Title | Enzyme-substrate complex structures of a GH39 beta-xylosidase from Geobacillus stearothermophilus. |
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Related PDB | 2bfg,2bs9 |
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Related UniProtKB | Q9ZFM2 |
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comments | This enzyme belongs to glycosidase family-39, with a retaining mechanism. According to the literature [6] and [7], the reaction proceeds as follows: (0) Arg52 and Tyr230 modulate the activity of catalytic nucleophile, Glu277, whereas His228 modulates the activity of a general acid-base, Glu160. (1) Glu160 acts as a general acid to protonate the leaving oxygen, O4 atom at subsite +1, forming an oxocarbenium-ion-like transition-state. The transition-state is stabilized by Asn159 and Tyr230 through hydrogen bonding to the oxygen atoms of xylose at subsite -1. (SN1-like reaction) (2) Glu277 makes a nucleophilic attack on C1 atom of substrate, xylan, to form a covalent intermediate with a xylose unit at the non-reducing end (or subsite -1). (3) Glu160 acts as a general base to deprotonate a water molecule, to activate it. (4) The activated water makes a nucleophilic attack on the C1 atom of the covalent intermediate. Thus, the substitution reaction completes.
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created | updated |
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2010-04-19 | 2012-01-27 |
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