1ABF

SUBSTRATE SPECIFICITY AND AFFINITY OF A PROTEIN MODULATED BY BOUND WATER MOLECULES

Summary for 1ABF

• Entry DOI: 10.2210/pdb1abf/pdb
• Descriptor: L-ARABINOSE-BINDING PROTEIN, alpha-D-fucopyranose, beta-D-fucopyranose, ... (4 entities in total)
• Functional Keywords: binding protein
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 33579.31

Authors

Wilson, D.K.,Quiocho, F.A. (deposition date: 1992-04-23, release date: 1993-10-31, Last modification date: 2024-02-07)

Primary citation

Quiocho, F.A.,Wilson, D.K.,Vyas, N.K.
Substrate specificity and affinity of a protein modulated by bound water molecules.
Nature, 340:404-407, 1989

PubMed Abstract: Water molecules influence molecular interactions in all biological systems, yet it is extremely difficult to understand their effects in precise atomic detail. Here we present evidence, based on highly refined atomic structures of the complexes of the L-arabinose-binding protein with L-arabinose, D-fucose and D-galactose, that bound water molecules, coupled with localized conformational changes, can govern substrate specificity and affinity. The atoms common to the three sugars are identically positioned in the binding site and the same nine strong hydrogen bonds are formed in all three complexes. Two hydrogen-bonded water molecules in the site contribute further to tight binding of L-arabinose but create an unfavourable interaction with the methyl group of D-fucose. Equally tight binding of D-galactose is attained by the replacement of one of the hydrogen-bonded water molecules by its--CH2OH group, coordinated with localized structural changes which include a shift and redirection of the hydrogen-bonding interactions of the other water molecule. These observations illustrate how ordered water molecules can contribute directly to the properties of proteins by influencing their interaction with ligands.

PubMed: 2818726
DOI: 10.1038/340404a0

Experimental method

X-RAY DIFFRACTION (1.9 Å)