TY - JOUR
T1 - The 1.6 Å crystal structure of the AraC sugar-binding and dimerization domain complexed with D-Fucose
AU - Soisson, Stephen M.
AU - MacDougall-Shackleton, Beth
AU - Schleif, Robert
AU - Wolberger, Cynthia
N1 - Funding Information:
We thank Elizabeth Reisinger for help in data collection and Craig Ogata of Beamline X4A for advice and technical support. Beamline X4A at the National Synchrotron Light Source, a DOE facility, is supported by the Howard Hughes Medical Institute. We thank Jeremy Berg for helpful comments on the manuscript. This work was supported by the Howard Hughes Medical Institute (C.W.), the David and Lucile Packard Foundation (C.W.), and grant GM18277 from the National Institutes of Health (R.S.).
PY - 1997/10/17
Y1 - 1997/10/17
N2 - The crystal structure of the sugar-binding and dimerization domain of the Escherichia coli gene regulatory protein, AraC, has been determined in complex with the competitive inhibitor D-fucose at pH 5.5 to a resolution of 1.6 Å. An in-depth analysis shows that the structural basis for AraC carbohydrate specificity arises from the precise arrangement of hydrogen bond-forming protein side-chains around the bound sugar molecule. van der Waals interactions also contribute to the epimeric and anomeric selectivity of the protein. The methyl group of D-fucose is accommodated by small side-chain movements in the sugar-binding site that result in a slight distortion in the positioning of the amino-terminal arm. A comparison of this structure with the 1.5 Å structure of AraC complexed with L-arabinose at neutral pH surprisingly revealed very small structural changes between the two complexes. Based on solution data, we suspect that the low pH used to crystallize the fucose complex affected the structure, and speculate about the nature of the changes between pH 5.5 and neutral pH and their implications for gene regulation by AraC. A comparison with the structurally unrelated E. coli periplasmic sugar-binding proteins reveals that conserved features of carbohydrate recognition are present, despite a complete lack of structural similarity between the two classes of proteins, suggesting convergent evolution of carbohydrate binding.
AB - The crystal structure of the sugar-binding and dimerization domain of the Escherichia coli gene regulatory protein, AraC, has been determined in complex with the competitive inhibitor D-fucose at pH 5.5 to a resolution of 1.6 Å. An in-depth analysis shows that the structural basis for AraC carbohydrate specificity arises from the precise arrangement of hydrogen bond-forming protein side-chains around the bound sugar molecule. van der Waals interactions also contribute to the epimeric and anomeric selectivity of the protein. The methyl group of D-fucose is accommodated by small side-chain movements in the sugar-binding site that result in a slight distortion in the positioning of the amino-terminal arm. A comparison of this structure with the 1.5 Å structure of AraC complexed with L-arabinose at neutral pH surprisingly revealed very small structural changes between the two complexes. Based on solution data, we suspect that the low pH used to crystallize the fucose complex affected the structure, and speculate about the nature of the changes between pH 5.5 and neutral pH and their implications for gene regulation by AraC. A comparison with the structurally unrelated E. coli periplasmic sugar-binding proteins reveals that conserved features of carbohydrate recognition are present, despite a complete lack of structural similarity between the two classes of proteins, suggesting convergent evolution of carbohydrate binding.
KW - AraC
KW - Arabinose
KW - Carbohydrate recognition
KW - Convergent evolution
KW - Fucose
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U2 - 10.1006/jmbi.1997.1314
DO - 10.1006/jmbi.1997.1314
M3 - Article
C2 - 9367758
AN - SCOPUS:0031576253
SN - 0022-2836
VL - 273
SP - 226
EP - 237
JO - Journal of molecular biology
JF - Journal of molecular biology
IS - 1
ER -