3W7S: Escherichia Coli K12 Ygjk Complexed With Glucose

Citation:
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.
PDB ID: 3W7SDownload
MMDB ID: 108795
PDB Deposition Date: 2013/3/6
Updated in MMDB: 2013/04
Experimental Method:
x-ray diffraction
Resolution: 1.9  Å
Source Organism:
Similar Structures:
Biological Unit for 3W7S: monomeric; determined by author and by software (PISA)
Molecular Components in 3W7S
Label Count Molecule
Protein (1 molecule)
1
Uncharacterized Protein Ygjk(Gene symbol: ygjK)
Molecule annotation
Chemicals (7 molecules)
1
1
2
6
* Click molecule labels to explore molecular sequence information.

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