Summary for 3W7S
| Entry DOI | 10.2210/pdb3w7s/pdb |
| Related | 3D3I 3W7T 3W7U |
| Descriptor | Uncharacterized protein YgjK, CALCIUM ION, alpha-D-glucopyranose, ... (4 entities in total) |
| Functional Keywords | gh63, processing alpha-glucosidase i, alpha/alpha barrel, hydrolase |
| Biological source | Escherichia coli |
| Total number of polymer chains | 2 |
| Total formula weight | 174071.51 |
| Authors | Miyazaki, T.,Kurakata, Y.,Uechi, A.,Yoshida, H.,Kamitori, S.,Sakano, Y.,Nishikawa, A.,Tonozuka, T. (deposition date: 2013-03-06, release date: 2013-04-03, Last modification date: 2020-07-29) |
| Primary citation | Kurakata, Y.,Uechi, A.,Yoshida, H.,Kamitori, S.,Sakano, Y.,Nishikawa, A.,Tonozuka, T. Structural insights into the substrate specificity and function of Escherichia coli K12 YgjK, a glucosidase belonging to the glycoside hydrolase family 63. J.Mol.Biol., 381:116-128, 2008 Cited by PubMed Abstract: Proteins belonging to the glycoside hydrolase family 63 (GH63) are found in bacteria, archaea, and eukaryotes. Eukaryotic GH63 proteins are processing *-glucosidase I enzymes that hydrolyze an oligosaccharide precursor of eukaryotic N-linked glycoproteins. In contrast, the functions of the bacterial and archaeal GH63 proteins are unclear. Here we determined the crystal structure of a bacterial GH63 enzyme, Escherichia coli K12 YgjK, at 1.78 A resolution and investigated some properties of the enzyme. YgjK consists of the N-domain and the A-domain, joined by a linker region. The N-domain is composed of 18 antiparallel beta-strands and is classified as a super-beta-sandwich. The A-domain contains 16 *-helices, 12 of which form an (*/*)(6)-barrel; the remaining 4 *-helices are found in an extra structural unit that we designated as the A'-region. YgjK, a member of the glycoside hydrolase clan GH-G, shares structural similarity with glucoamylase (GH15) and chitobiose phosphorylase (GH94) [corrected] both of which belong to clan GH-L or GH-L-like [corrected] In crystal structures of YgjK in complex with glucose, mannose, and galactose, all of the glucose, mannose, and galactose units were located in the catalytic cleft. YgjK showed the highest activity for the *-1,3-glucosidic linkage of nigerose, but also hydrolyzed trehalose, kojibiose, and maltooligosaccharides from maltose to maltoheptaose, although the activities were low. These findings suggest that YgjK is a glucosidase with relaxed specificity for sugars. PubMed: 18586271DOI: 10.1016/j.jmb.2008.05.061 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.9 Å) |
Structure validation
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