6H76

SiaP in complex with Neu5Ac (RT)

Summary for 6H76

• Entry DOI: 10.2210/pdb6h76/pdb
• Descriptor: Sialic acid-binding periplasmic protein SiaP, N-acetyl-beta-neuraminic acid, CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: trap transporter, sialic acid, transport protein
• Biological source: Haemophilus influenzae Rd KW20
• Total number of polymer chains: 1
• Total formula weight: 35678.60

Authors

Fischer, M.,Darby, J.F.,Brannigan, J.A.,Turkenburg, J.,Hubbard, R.E. (deposition date: 2018-07-30, release date: 2019-08-14, Last modification date: 2024-05-15)

Primary citation

Darby, J.F.,Hopkins, A.P.,Shimizu, S.,Roberts, S.M.,Brannigan, J.A.,Turkenburg, J.P.,Thomas, G.H.,Hubbard, R.E.,Fischer, M.
Water Networks Can Determine the Affinity of Ligand Binding to Proteins.
J.Am.Chem.Soc., 141:15818-15826, 2019

PubMed Abstract: Solvent organization is a key but underexploited contributor to the thermodynamics of protein-ligand recognition, with implications for ligand discovery, drug resistance, and protein engineering. Here, we explore the contribution of solvent to ligand binding in the virulence protein SiaP. By introducing a single mutation without direct ligand contacts, we observed a >1000-fold change in sialic acid binding affinity. Crystallographic and calorimetric data of wild-type and mutant SiaP showed that this change results from an enthalpically unfavorable perturbation of the solvent network. This disruption is reflected by changes in the normalized atomic displacement parameters of crystallographic water molecules. In SiaP's enclosed cavity, relative differences in water-network dynamics serve as a simple predictor of changes in the free energy of binding upon changing protein, ligand, or both. This suggests that solvent structure is an evolutionary constraint on protein sequence that contributes to ligand affinity and selectivity.

PubMed: 31518131
DOI: 10.1021/jacs.9b06275

Experimental method

X-RAY DIFFRACTION (1.5 Å)