3UR7

Higher-density crystal structure of potato endo-1,3-beta-glucanase

Summary for 3UR7

• Entry DOI: 10.2210/pdb3ur7/pdb
• Related: 1GHS 2CYG 3EM5 3F55 3UR8
• Descriptor: Glucan endo-1,3-beta-D-glucosidase, SODIUM ION (3 entities in total)
• Functional Keywords: glucoside hydrolase, gh17 family, pathogenesis-related class-2 protein (pr-2), tim barrel, hydrolase, carbohydrate/sugar binding
• Biological source: Solanum tuberosum (potatoes)
• Total number of polymer chains: 2
• Total formula weight: 73240.93

Authors

Wojtkowiak, A.,Witek, K.,Hennig, J.,Jaskolski, M. (deposition date: 2011-11-21, release date: 2012-05-30, Last modification date: 2023-09-13)

Primary citation

Wojtkowiak, A.,Witek, K.,Hennig, J.,Jaskolski, M.
Two high-resolution structures of potato endo-1,3-beta-glucanase reveal subdomain flexibility with implications for substrate binding
Acta Crystallogr.,Sect.D, 68:713-723, 2012

PubMed Abstract: Endo-1,3-β-glucanases are widely distributed among bacteria, fungi and higher plants. They are responsible for hydrolysis of the glycosidic bond in specific polysaccharides with tracts of unsubstituted β-1,3-linked glucosyl residues. The plant enzymes belong to glycoside hydrolase family 17 (GH17) and are also members of class 2 of pathogenesis-related (PR) proteins. X-ray diffraction data were collected to 1.40 and 1.26 Å resolution from two crystals of endo-1,3-β-glucanase from Solanum tuberosum (potato, cultivar Désirée) which, despite having a similar packing framework, represented two separate crystal forms. In particular, they differed in the Matthews coefficient and are consequently referred to as higher density (HD; 1.40 Å resolution) and lower density (LD; 1.26 Å resolution) forms. The general fold of the protein resembles that of other known plant endo-1,3-β-glucanases and is defined by a (β/α)(8)-barrel with an additional subdomain built around the C-terminal half of the barrel. The structures revealed high flexibility of the subdomain, which forms part of the catalytic cleft. Comparison with structures of other GH17 endo-1,3-β-glucanases revealed differences in the arrangement of the secondary-structure elements in this region, which can be correlated with sequence variability and may suggest distinct substrate-binding patterns. The crystal structures revealed an unusual packing mode, clearly visible in the LD structure, caused by the presence of the C-terminal His(6) tag, which extends from the compact fold of the enzyme molecule and docks in the catalytic cleft of a neighbouring molecule. In this way, an infinite chain of His-tag-linked protein molecules is formed along the c direction.

PubMed: 22683794
DOI: 10.1107/S090744491200995X

Experimental method

X-RAY DIFFRACTION (1.4 Å)