DB code: D00844
| RLCP classification | 1.30.35885.972 : Hydrolysis | |
|---|---|---|
| CATH domain | 2.60.40.1500 : Immunoglobulin-like | |
| 3.20.20.80 : TIM Barrel | Catalytic domain | |
| E.C. | 3.2.1.37 | |
| CSA | ||
| M-CSA | ||
| MACiE | ||
| CATH domain | Related DB codes (homologues) |
|---|---|
| 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 |
| Uniprot Enzyme Name | UniprotKB | Protein name | Synonyms | CAZy | Pfam |
|---|---|---|---|---|
| P36906 |
Beta-xylosidase
|
EC
3.2.1.37
1,4-beta-D-xylan xylohydrolase Xylan 1,4-beta-xylosidase |
GH39
(Glycoside Hydrolase Family 39)
|
PF01229
(Glyco_hydro_39)
[Graphical View] |
| Q9ZFM2 |
Beta-xylosidase
|
EC
3.2.1.37
1,4-beta-D-xylan xylohydrolase Xylan 1,4-beta-xylosidase |
GH39
(Glycoside Hydrolase Family 39)
|
PF01229
(Glyco_hydro_39)
[Graphical View] |
| KEGG enzyme name |
|---|
|
Xylan 1,4-beta-xylosidase
Xylobiase Beta-xylosidase Exo-1,4-beta-xylosidase Beta-D-xylopyranosidase Beta-xylosidase Beta-xylosidase Exo-1,4-xylosidase Exo-1,4-beta-D-xylosidase 1,4-beta-D-xylan xylohydrolase |
| UniprotKB: Accession Number | Entry name | Activity | Subunit | Subcellular location | Cofactor |
|---|---|---|---|---|---|
| P36906 | XYNB_THESA | Hydrolysis of 1,4-beta-D-xylans, to remove successive D-xylose residues from the non-reducing termini. | |||
| Q9ZFM2 | XYNB_BACST | Hydrolysis of 1,4-beta-D-xylans, to remove successive D-xylose residues from the non-reducing termini. |
| KEGG Pathways | Map code | Pathways | E.C. |
|---|---|---|
| MAP00500 | Starch and sucrose metabolism | |
| MAP00520 | Nucleotide sugars metabolism |
| Compound table | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Substrates | Products | Intermediates | ||||||||||||
| KEGG-id | L00052 | C02352 | C02337 | C00001 | L00052 | C02352 | C02337 | C02096 | I00061 | |||||
| E.C. | ||||||||||||||
| 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 | |||||
| Type | aromatic ring (only carbon atom),carboxyl group,polysaccharide | polysaccharide | polysaccharide | H2O | aromatic ring (only carbon atom),carboxyl group,polysaccharide | polysaccharide | polysaccharide | carbohydrate | ||||||
| ChEBI |
15377 15377 |
28161 28161 |
||||||||||||
| PubChem |
22247451 962 22247451 962 |
125409 125409 |
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| 1px8A01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1px8B01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1uhvA01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1uhvB01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1uhvC01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1uhvD01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1w91A01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1w91B01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1w91C01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1w91D01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1w91E01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1w91F01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1w91G01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1w91H01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bfgA01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bfgB01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bfgC01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bfgD01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bfgE01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bfgF01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bfgG01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bfgH01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bs9A01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bs9B01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bs9C01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bs9D01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bs9E01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bs9F01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bs9G01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bs9H01 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1px8A02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Bound:XYP | Unbound | |
| 1px8B02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Bound:XYP | Unbound | |
| 1uhvA02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Intermediate-analogue:DFX | |
| 1uhvB02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Intermediate-analogue:DFX | |
| 1uhvC02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Intermediate-analogue:DFX | |
| 1uhvD02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Intermediate-analogue:DFX | |
| 1w91A02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1w91B02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1w91C02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1w91D02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1w91E02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1w91F02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1w91G02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1w91H02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bfgA02 |
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Unbound | Unbound | Analogue:ANX-XYP | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:XYS | |
| 2bfgB02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:XYS | |
| 2bfgC02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:XYS | |
| 2bfgD02 |
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Unbound | Unbound | Analogue:ANX-XYP | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:XYS | |
| 2bfgE02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:XYS | |
| 2bfgF02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:XYS | |
| 2bfgG02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:XYS | |
| 2bfgH02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Intermediate-bound:XYS | |
| 2bs9A02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bs9B02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bs9C02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bs9D02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bs9E02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bs9F02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bs9G02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 2bs9H02 |
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| Reference for Active-site residues | ||
|---|---|---|
| resource | references | E.C. |
| Literature [5], [6], [7] & Swiss-prot;P36906, Q9ZFM2 | ||
| Active-site residues | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| PDB | Catalytic residues | Cofactor-binding residues | Modified residues | Main-chain involved in catalysis | Comment | |||||
| 1px8A01 |
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| 1px8B01 |
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| 1uhvA01 |
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| 1uhvB01 |
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| 1uhvC01 |
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| 1uhvD01 |
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| 1w91A01 |
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| 1w91B01 |
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| 1w91C01 |
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| 1w91D01 |
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| 1w91E01 |
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| 1w91F01 |
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| 1w91G01 |
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| 1w91H01 |
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| 2bfgA01 |
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| 2bfgB01 |
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| 2bfgC01 |
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| 2bfgD01 |
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| 2bfgE01 |
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| 2bfgF01 |
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| 2bfgG01 |
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| 2bfgH01 |
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| 2bs9A01 |
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| 2bs9B01 |
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| 2bs9C01 |
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| 2bs9D01 |
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| 2bs9E01 |
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| 2bs9F01 |
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| 2bs9G01 |
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| 2bs9H01 |
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| 1px8A02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 277 | ||||
| 1px8B02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 277 | ||||
| 1uhvA02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 277 | ||||
| 1uhvB02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 277 | ||||
| 1uhvC02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 277 | ||||
| 1uhvD02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 277 | ||||
| 1w91A02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278 | ||||
| 1w91B02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278 | ||||
| 1w91C02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278 | ||||
| 1w91D02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278 | ||||
| 1w91E02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278 | ||||
| 1w91F02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278 | ||||
| 1w91G02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278 | ||||
| 1w91H02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278 | ||||
| 2bfgA02 |
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ARG 52;ASN 159;;HIS 228;TYR 230;GLU 278 | mutant E160A | |||
| 2bfgB02 |
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ARG 52;ASN 159;;HIS 228;TYR 230;GLU 278 | mutant E160A | |||
| 2bfgC02 |
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ARG 52;ASN 159;;HIS 228;TYR 230;GLU 278 | mutant E160A | |||
| 2bfgD02 |
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ARG 52;ASN 159;;HIS 228;TYR 230;GLU 278 | mutant E160A | |||
| 2bfgE02 |
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ARG 52;ASN 159;;HIS 228;TYR 230;GLU 278 | mutant E160A | |||
| 2bfgF02 |
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ARG 52;ASN 159;;HIS 228;TYR 230;GLU 278 | mutant E160A | |||
| 2bfgG02 |
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ARG 52;ASN 159;;HIS 228;TYR 230;GLU 278 | mutant E160A | |||
| 2bfgH02 |
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ARG 52;ASN 159;;HIS 228;TYR 230;GLU 278 | mutant E160A | |||
| 2bs9A02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278 | ||||
| 2bs9B02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278 | ||||
| 2bs9C02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278 | ||||
| 2bs9D02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278 | ||||
| 2bs9E02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278 | ||||
| 2bs9F02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278 | ||||
| 2bs9G02 |
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278 | ||||
| 2bs9H02 |
|
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ARG 52;ASN 159;GLU 160;HIS 228;TYR 230;GLU 278 | ||||
| References for Catalytic Mechanism | ||
|---|---|---|
| References | Sections | No. of steps in catalysis |
|
[5]
|
Scheme 1 | |
|
[6]
|
Figure 5, p.159-162 | |
|
[7]
|
Figure 4, p.841-844 | |
| References | |
|---|---|
| [1] | |
| Resource | |
| Comments | CHARACTERIZATION. |
| Medline ID | |
| PubMed ID | 8612648 |
| Journal | Eur J Biochem |
| Year | 1996 |
| Volume | 236 |
| Pages | 706-13 |
| Authors | Armand S, Vieille C, Gey C, Heyraud A, Zeikus JG, Henrissat B |
| Title | Stereochemical course and reaction products of the action of beta-xylosidase from Thermoanaerobacterium saccharolyticum strain B6A-RI. |
| Related PDB | |
| Related UniProtKB | |
| [2] | |
| Resource | |
| Comments |
ACTIVE SITE GLU-277, |
| Medline ID | |
| PubMed ID | 9761746 |
| Journal | Biochem J |
| Year | 1998 |
| Volume | 335 |
| Pages | 449-55 |
| Authors | Vocadlo DJ, MacKenzie LF, He S, Zeikus GJ, Withers SG |
| Title | Identification of glu-277 as the catalytic nucleophile of Thermoanaerobacterium saccharolyticum beta-xylosidase using electrospray MS. |
| Related PDB | |
| Related UniProtKB | |
| [3] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11322958 |
| Journal | FEBS Lett |
| Year | 2001 |
| Volume | 495 |
| Pages | 115-9 |
| Authors | Bravman T, Mechaly A, Shulami S, Belakhov V, Baasov T, Shoham G, Shoham Y |
| Title | Glutamic acid 160 is the acid-base catalyst of beta-xylosidase from Bacillus stearothermophilus T-6: a family 39 glycoside hydrolase. |
| Related PDB | |
| Related UniProtKB | |
| [4] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 12146939 |
| Journal | Biochemistry |
| Year | 2002 |
| Volume | 41 |
| Pages | 9736-46 |
| Authors | Vocadlo DJ, Wicki J, Rupitz K, Withers SG |
| 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. |
| Related PDB | |
| Related UniProtKB | |
| [5] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 12146938 |
| Journal | Biochemistry |
| Year | 2002 |
| Volume | 41 |
| Pages | 9727-35 |
| Authors | Vocadlo DJ, Wicki J, Rupitz K, Withers SG |
| Title | Mechanism of Thermoanaerobacterium saccharolyticum beta-xylosidase: kinetic studies. |
| Related PDB | |
| Related UniProtKB | |
| [6] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) |
| Medline ID | |
| PubMed ID | 14659747 |
| Journal | J Mol Biol |
| Year | 2004 |
| Volume | 335 |
| Pages | 155-65 |
| 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 |
| Title |
Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, |
| Related PDB | 1px8 1uhv |
| Related UniProtKB | P36906 |
| [7] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) |
| Medline ID | |
| PubMed ID | 16212978 |
| Journal | J Mol Biol |
| Year | 2005 |
| Volume | 353 |
| Pages | 838-46 |
| Authors | Czjzek M, Ben David A, Bravman T, Shoham G, Henrissat B, Shoham Y |
| Title | Enzyme-substrate complex structures of a GH39 beta-xylosidase from Geobacillus stearothermophilus. |
| Related PDB | 2bfg 2bs9 |
| Related UniProtKB | Q9ZFM2 |
| Comments |
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This enzyme belongs to glycosidase family-39, According to the literature [6] and [7], (0) Arg52 and Tyr230 modulate the activity of catalytic nucleophile, (1) Glu160 acts as a general acid to protonate the leaving oxygen, (2) Glu277 makes a nucleophilic attack on C1 atom of substrate, (3) Glu160 acts as a general base to deprotonate a water molecule, (4) The activated water makes a nucleophilic attack on the C1 atom of the covalent intermediate. |
| Created | Updated |
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| 2010-04-19 | 2012-01-27 |