5DVI

High resolution crystal Structure of glucose complexed periplasmic glucose binding protein (ppGBP) from P. putida CSV86

Summary for 5DVI

• Entry DOI: 10.2210/pdb5dvi/pdb
• Related: 5DVF 5DVJ
• Descriptor: Binding protein component of ABC sugar transporter, beta-D-glucopyranose, GLYCEROL, ... (5 entities in total)
• Functional Keywords: periplasmic glucose binding protein, ppgbp, crystallization, sugar transport, sugar binding pocket, sugar abc transporter, transport protein
• Biological source: Pseudomonas putida CSV86
• Total number of polymer chains: 2
• Total formula weight: 91627.00

Authors

Pandey, S.,Modak, A.,Phale, P.S.,Bhaumik, P. (deposition date: 2015-09-21, release date: 2016-02-24, Last modification date: 2024-11-13)

Primary citation

Pandey, S.,Modak, A.,Phale, P.S.,Bhaumik, P.
High Resolution Structures of Periplasmic Glucose-binding Protein of Pseudomonas putida CSV86 Reveal Structural Basis of Its Substrate Specificity
J.Biol.Chem., 291:7844-7857, 2016

PubMed Abstract: Periplasmic substrate-binding proteins (SBPs) bind to the specific ligand with high affinity and mediate their transport into the cytoplasm via the cognate inner membrane ATP-binding cassette proteins. Because of low sequence identities, understanding the structural basis of substrate recognition by SBPs has remained very challenging. There are several structures available for the ligand-bound sugar SBPs, but very few unliganded structures are reported. No structural data are available for sugar SBPs fromPseudomonassp. to date. This study reports the first high resolution crystal structures of periplasmic glucose-binding protein fromPseudomonas putidaCSV86 (ppGBP) in unliganded form (2.5 Å) and complexed with glucose (1.25 Å) and galactose (1.8 Å). Asymmetric domain closure of ppGBP was observed upon substrate binding. The ppGBP was found to have an affinity of ∼ 0.3 μmfor glucose. The structural analysis showed that the sugars are bound to the protein mainly by hydrogen bonds, and the loss of two strong hydrogen bonds between ppGBP and galactose compared with glucose may be responsible for lowering its affinity toward galactose. The higher stability of ppGBP-glucose complex was also indicated by an 8 °C increase in the melting temperature compared with unliganded form and ppGBP-galactose complex. ppGBP binds to monosaccharide, but the structural features revealed it to have an oligosaccharide-binding protein fold, indicating that during evolution the sugar binding pocket may have undergone structural modulation to accommodate monosaccharide only.

PubMed: 26861882
DOI: 10.1074/jbc.M115.697268

Experimental method

X-RAY DIFFRACTION (1.25 Å)