6WPN

Crystal structure of a putative oligosaccharide periplasmic-binding protein from Synechococcus sp. MITs9220

Summary for 6WPN

• Entry DOI: 10.2210/pdb6wpn/pdb
• Related: 6WPM
• Descriptor: Substrate-binding protein, 1,2-ETHANEDIOL, GLYCEROL, ... (4 entities in total)
• Functional Keywords: substrate-binding protein, marine cyanobacteria, sugar-binding protein, transport protein
• Biological source: Synechococcus sp.
• Total number of polymer chains: 2
• Total formula weight: 94991.10

Authors

Ford, B.A.,Michie, K.A.,Paulsen, I.T.,Mabbutt, B.C.,Shah, B.S. (deposition date: 2020-04-27, release date: 2021-05-12, Last modification date: 2024-10-23)

Primary citation

Ford, B.A.,Michie, K.A.,Paulsen, I.T.,Mabbutt, B.C.,Shah, B.S.
Novel functional insights into a modified sugar-binding protein from Synechococcus MITS9220.
Sci Rep, 12:4805-4805, 2022

PubMed Abstract: Paradigms of metabolic strategies employed by photoautotrophic marine picocyanobacteria have been challenged in recent years. Based on genomic annotations, picocyanobacteria are predicted to assimilate organic nutrients via ATP-binding cassette importers, a process mediated by substrate-binding proteins. We report the functional characterisation of a modified sugar-binding protein, MsBP, from a marine Synechococcus strain, MITS9220. Ligand screening of MsBP shows a specific affinity for zinc (K ~ 1.3 μM) and a preference for phosphate-modified sugars, such as fructose-1,6-biphosphate, in the presence of zinc (K ~ 5.8 μM). Our crystal structures of apo MsBP (no zinc or substrate-bound) and Zn-MsBP (with zinc-bound) show that the presence of zinc induces structural differences, leading to a partially-closed substrate-binding cavity. The Zn-MsBP structure also sequesters several sulphate ions from the crystallisation condition, including two in the binding cleft, appropriately placed to mimic the orientation of adducts of a biphosphate hexose. Combined with a previously unseen positively charged binding cleft in our two structures and our binding affinity data, these observations highlight novel molecular variations on the sugar-binding SBP scaffold. Our findings lend further evidence to a proposed sugar acquisition mechanism in picocyanobacteria alluding to a mixotrophic strategy within these ubiquitous photosynthetic bacteria.

PubMed: 35314715
DOI: 10.1038/s41598-022-08459-8

Experimental method

X-RAY DIFFRACTION (2.29 Å)