5ZI9
Crystal structure of type-II LOG from Streptomyces coelicolor A3
Summary for 5ZI9
| Entry DOI | 10.2210/pdb5zi9/pdb |
| Descriptor | Cytokinin riboside 5'-monophosphate phosphoribohydrolase, 1,2-ETHANEDIOL, CITRATE ANION, ... (5 entities in total) |
| Functional Keywords | hydrolase |
| Biological source | Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) |
| Total number of polymer chains | 4 |
| Total formula weight | 116209.21 |
| Authors | Seo, H.,Kim, K.-J. (deposition date: 2018-03-14, release date: 2018-04-18, Last modification date: 2023-11-22) |
| Primary citation | Seo, H.,Kim, K.J. Structural and biochemical characterization of the type-II LOG protein from Streptomyces coelicolor A3. Biochem. Biophys. Res. Commun., 499:577-583, 2018 Cited by PubMed Abstract: Streptomyces coelicolor A3 contains Sc5140, a gene coding for poorly understood bacterial LOG-like protein. In this study, we determined the crystal structure of Sc5140 and found it resembles the overall structure of other type-II LOGs. In addition, Sc5140 exhibited phosphoribohydrolase activity against adenosine monophosphate (AMP), indicating that it had the same function as known type-II LOGs. Based on these results, we designated Sc5140 as ScLOGII. We performed docking calculations of AMP into the ScLOGII structure, which suggested the mode of binding for type-II LOG with their AMP substrate. The ScLOGII structure uniquely exhibited a long tail-like structure at the N-terminus that was involved in hexamerization of the protein; the disordered N-terminal region (DNR). Truncation of DNR in ScLOGII negatively affected both the phosphoribohydrolase activity and the oligomerization of the protein, suggesting that this region functioned in enzyme stabilization. However, results from truncation experiments using ScLOGII and CgLOGII, a type-II LOG homologue from Corynebacterium glutamicum, were quite different, leaving uncertainty regarding the general functions of DNR in type-II LOGs. Overall, the current structural work may help in understand the significance of type-II LOG protein at the molecular level. PubMed: 29596827DOI: 10.1016/j.bbrc.2018.03.193 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.5 Å) |
Structure validation
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