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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,S00915,M00134,M00160,D00479,S00204,S00205,S00206,S00207,S00203,S00208,S00209,S00211,S00213,S00214,M00113,T00307,D00165,D00166,D00169,D00176,D00501,D00502,D00503,D00844,D00861,D00864,M00026,M00112,M00193,M00346,T00057,T00062,T00063,T00066,T00067 |
UniProtKB:Accession Number | Q65CX5 |
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Entry name | GANA_BACLD |
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Activity | Endohydrolysis of 1,4-beta-D-galactosidic linkages in arabinogalactans. |
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Subunit |
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Subcellular location |
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Cofactor | Binds 1 calcium ion per subunit. |
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Compound table: links to PDB-related databases & PoSSuM |
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| Cofactors | Substrates | Products | intermediates |
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KEGG-id | C00076 | L00048 | L00049 | C05796 | C00001 | L00048 | L00049 | C05796 | C03611 | I00121 |
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Compound | Calcium | Rhamnogalacturonan I | Arabinogalactan type I | Galactan | H2O | Rhamnogalacturonan I | Arabinogalactan | Galactan | Galactose oligosaccharide | Peptidyl-Glu-galactan |
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Type | divalent metal (Ca2+, Mg2+) | carboxyl group,polysaccharide | polysaccharide | polysaccharide | H2O | carboxyl group,polysaccharide | polysaccharide | polysaccharide | polysaccharide |
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ChEBI | 29108
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| 15377
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PubChem | 271
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| 22247451 962
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1r8lA00 |  |  |  |  |  |  |  | Bound:_CA | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1r8lB00 |  |  |  |  |  |  |  | Bound:_CA | Unbound | Unbound | Unbound | | Unbound | Unbound | Unbound | Unbound | Unbound |
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1ur0A00 |  |  |  |  |  |  |  | Bound:_CA | Unbound | Unbound | Unbound | | Unbound | Unbound | Bound:B4G | Unbound | Unbound |
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1ur0B00 |  |  |  |  |  |  |  | Bound:_CA | Unbound | Unbound | Unbound | | Unbound | Unbound | Bound:B4G | Unbound | Unbound |
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1ur4A00 |  |  |  |  |  |  |  | Bound:_CA | Unbound | Unbound | Unbound | | Unbound | Unbound | Bound:B2G | Unbound | Unbound |
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1ur4B00 |  |  |  |  |  |  |  | Bound:_CA | Unbound | Unbound | Unbound | | Unbound | Unbound | Bound:B2G | Unbound | Unbound |
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2ccrA00 |  |  |  |  |  |  |  | Bound:_CA | Unbound | Unbound | Unbound | | Unbound | Unbound | Bound:B4G | Bound:B2G | Unbound |
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2ccrB00 |  |  |  |  |  |  |  | Bound:_CA | Unbound | Unbound | Unbound | | Unbound | Unbound | Bound:B4G | Bound:B2G | Unbound |
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2gftA00 |  |  |  |  |  |  |  | Bound:_CA | Unbound | Unbound | Unbound | | Unbound | Unbound | Bound:GAL-GAL-GAL | Unbound | Unbound |
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2gftB00 |  |  |  |  |  |  |  | Bound:_CA | Unbound | Unbound | Unbound | | Unbound | Unbound | Bound:GAL-GAL-GAL | Unbound | Unbound |
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2j74A00 |  |  |  |  |  |  |  | Bound:_CA | Unbound | Unbound | Unbound | | Unbound | Unbound | Bound:B4G | Bound:B2G | Unbound |
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2j74B00 |  |  |  |  |  |  |  | Bound:_CA | Unbound | Unbound | Unbound | | Unbound | Unbound | Bound:B4G | Bound:B2G | Unbound |
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References for Catalytic Mechanism | References | Sections | No. of steps in catalysis |
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[6] | FIGURE 3, p.15138-15141 |
| [8] | Figure 5 |
| [9] | p.109 |
| [11] | p.978 |
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references | [1] |
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PubMed ID | 823153 |
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Journal | J Biol Chem |
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Year | 1976 |
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Volume | 251 |
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Pages | 5904-10 |
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Authors | Labavitch JM, Freeman LE, Albersheim P |
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Title | Structure of plant cell walls. Purification and characterization of a beta-1,4-galactanase which degrades a structural component of the primary cell walls of dicots. |
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[2] |
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Journal | Carbohydr Polym |
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Year | 1991 |
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Volume | 16 |
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Pages | 167-87 |
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Authors | van de Visa JW, Searle-van Leeuwena MJF, Silihaa HA, Kormelinka FJM, Voragena AGJ |
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Title | Purification and characterization of Endo-1,4-beta-D-galactanases from Aspergillus niger and Aspergillus aculeatus: Use in combination with arabinanases from Aspergillus niger in enzymic conversion of potato arabinogalactan |
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[3] |
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PubMed ID | 7712292 |
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Journal | Curr Opin Struct Biol |
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Year | 1994 |
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Volume | 4 |
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Pages | 885-92 |
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Authors | McCarter JD, Withers SG |
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Title | Mechanisms of enzymatic glycoside hydrolysis. |
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[4] |
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PubMed ID | 8535779 |
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Journal | Structure |
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Year | 1995 |
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Volume | 3 |
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Pages | 853-9 |
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Authors | Davies G, Henrissat B |
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Title | Structures and mechanisms of glycosyl hydrolases. |
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[5] |
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PubMed ID | 9398278 |
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Journal | Biochemistry |
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Year | 1997 |
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Volume | 36 |
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Pages | 15489-500 |
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Authors | Braithwaite KL, Barna T, Spurway TD, Charnock SJ, Black GW, Hughes N, Lakey JH, Virden R, Hazlewood GP, Henrissat B, Gilbert HJ |
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Title | Evidence that galactanase A from Pseudomonas fluorescens subspecies cellulosa is a retaining family 53 glycosyl hydrolase in which E161 and E270 are the catalytic residues. |
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[6] |
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Comments | X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS). |
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PubMed ID | 12484750 |
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Journal | Biochemistry |
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Year | 2002 |
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Volume | 41 |
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Pages | 15135-43 |
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Authors | Ryttersgaard C, Lo Leggio L, Coutinho PM, Henrissat B, Larsen S |
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Title | Aspergillus aculeatus beta-1,4-galactanase: substrate recognition and relations to other glycoside hydrolases in clan GH-A. |
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Related PDB | 1fhl,1fob |
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Related UniProtKB | P48842 |
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[7] |
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Journal | Carbohydr Polym |
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Year | 2003 |
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Volume | 53 |
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Pages | 155-68 |
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Authors | Luonteria E, Laineb C, Uusitaloa S, Telemanc A, Siika-ahoa M, Tenkanen M |
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Title | Purification and characterization of Aspergillus beta-D-galactanases acting on beta-1,4- and beta-1,3/6-linked arabinogalactans |
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[8] |
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Comments | X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS), CATALYTIC ACTIVITY, GLYCOSYLATION AT ASN-111. |
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PubMed ID | 12761390 |
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Journal | Protein Sci |
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Year | 2003 |
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Volume | 12 |
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Pages | 1195-204 |
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Authors | Le Nours J, Ryttersgaard C, Lo Leggio L, Ostergaard PR, Borchert TV, Christensen LL, Larsen S |
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Title | Structure of two fungal beta-1,4-galactanases: searching for the basis for temperature and pH optimum. |
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Related PDB | 1hjq,1hjs,1hju |
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Related UniProtKB | P83691,P83692 |
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[9] |
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Comments | X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 28-424 IN COMPLEX WITH CALCIUM IONS AND SUBSTRATE ANALOGS, COFACTOR. |
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PubMed ID | 15312766 |
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Journal | J Mol Biol |
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Year | 2004 |
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Volume | 341 |
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Pages | 107-17 |
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Authors | Ryttersgaard C, Le Nours J, Lo Leggio L, Jorgensen CT, Christensen LL, Bjornvad M, Larsen S |
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Title | The structure of endo-beta-1,4-galactanase from Bacillus licheniformis in complex with two oligosaccharide products. |
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Related PDB | 1r8l,1ur0,1ur4 |
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Related UniProtKB | Q65CX5 |
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[10] |
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PubMed ID | 16151143 |
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Journal | Appl Environ Microbiol |
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Year | 2005 |
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Volume | 71 |
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Pages | 5501-10 |
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Authors | Hinz SW, Pastink MI, van den Broek LA, Vincken JP, Voragen AG |
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Title | Bifidobacterium longum endogalactanase liberates galactotriose from type I galactans. |
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[11] |
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PubMed ID | 19089956 |
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Journal | Proteins |
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Year | 2009 |
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Volume | 75 |
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Pages | 977-89 |
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Authors | Le Nours J, De Maria L, Welner D, Jorgensen CT, Christensen LL, Borchert TV, Larsen S, Lo Leggio L |
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Title | Investigating the binding of beta-1,4-galactan to Bacillus licheniformis beta-1,4-galactanase by crystallography and computational modeling. |
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Related PDB | 2ccr,2j74 |
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Related UniProtKB | Q65CX5 |
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comments | This enzyme belongs to glycosidase family-58, with a retaining mechanism. This enzyme is homologous to a counterpart enzyme from fungi (S00748 in EzCatDB). Although this enzyme binds calcium ion, it is not involved in catalysis. The reactiom mechanism must be similar to that of the homologous enzyme. According to the literature [6], the reaction mechanism proceeds as follows: (0) Arg66 and Tyr234 modulate the pKa of catalytic nucleophile, Glu263. (1) Glu165 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 Asn164 and Tyr234 through hydrogen bonding to the oxygen atoms at subsite -1. (SN1-like reaction) (2) Glu263 makes a nucleophilic attack on C1 atom of substrate, galactan, to form a covalent intermediate. (3) Glu165 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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2010-04-08 | 2018-04-23 |
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