5GHL
Crystal structure Analysis of the starch-binding domain of glucoamylase from Aspergillus niger
Summary for 5GHL
| Entry DOI | 10.2210/pdb5ghl/pdb |
| Descriptor | Glucoamylase, GLYCEROL, SULFATE ION, ... (4 entities in total) |
| Functional Keywords | beta-sheet structure, hydrolase |
| Biological source | Aspergillus niger |
| Total number of polymer chains | 4 |
| Total formula weight | 48291.91 |
| Authors | Miyake, H.,Suyama, Y.,Muraki, N.,Kusunoki, M.,Tanaka, A. (deposition date: 2016-06-20, release date: 2017-10-18, Last modification date: 2024-10-23) |
| Primary citation | Suyama, Y.,Muraki, N.,Kusunoki, M.,Miyake, H. Crystal structure of the starch-binding domain of glucoamylase from Aspergillus niger. Acta Crystallogr.,Sect.F, 73:550-554, 2017 Cited by PubMed Abstract: Glucoamylases are widely used commercially to produce glucose syrup from starch. The starch-binding domain (SBD) of glucoamylase from Aspergillus niger is a small globular protein containing a disulfide bond. The structure of A. niger SBD has been determined by NMR, but the conformation surrounding the disulfide bond was unclear. Therefore, X-ray crystal structural analysis was used to attempt to clarify the conformation of this region. The SBD was purified from an Escherichia coli-based expression system and crystallized at 293 K. The initial phase was determined by the molecular-replacement method, and the asymmetric unit of the crystal contained four protomers, two of which were related by a noncrystallographic twofold axis. Finally, the structure was solved at 2.0 Å resolution. The SBD consisted of seven β-strands and eight loops, and the conformation surrounding the disulfide bond was determined from a clear electron-density map. Comparison of X-ray- and NMR-determined structures of the free SBD showed no significant difference in the conformation of each β-strand, but the conformations of the loops containing the disulfide bond and the L5 loop were different. In particular, the difference in the position of the C atom of Cys509 between the X-ray- and NMR-determined structures was 13.3 Å. In addition, the B factors of the amino-acid residues surrounding the disulfide bond are higher than those of other residues. Therefore, the conformation surrounding the disulfide bond is suggested to be highly flexible. PubMed: 28994402DOI: 10.1107/S2053230X17012894 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2 Å) |
Structure validation
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