Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli.
Structural proteomics projects are generating three-dimensional structures of novel, uncharacterized proteins at an increasing rate. However, structure alone is often insufficient to deduce the specific biochemical function of a protein. Here we determined the function for a protein using a strategy that integrates structural and bioinformatics data with parallel experimental screening for enzymatic activity. BioH is involved in biotin biosynthesis in Escherichia coli and had no previously known biochemical function. The crystal structure of BioH was determined at 1.7 A resolution. An automated procedure was used to compare the structure of BioH with structural templates from a variety of different enzyme active sites. This screen identified a catalytic triad (Ser82, His235, and Asp207) with a configuration similar to that of the catalytic triad of hydrolases. Analysis of BioH with a panel of hydrolase assays revealed a carboxylesterase activity with a preference for short acyl chain substrates. The combined use of structural bioinformatics with experimental screens for detecting enzyme activity could greatly enhance the rate at which function is determined from structure.
Sanishvili
Ruslan
R
Biosciences Division, Argonne National Laboratory, Argonne, Illinois, 60439, USA.
Yakunin
Alexander F
AF
Laskowski
Roman A
RA
Skarina
Tatiana
T
Evdokimova
Elena
E
Doherty-Kirby
Amanda
A
Lajoie
Gilles A
GA
Thornton
Janet M
JM
Arrowsmith
Cheryl H
CH
Savchenko
Alexei
A
Joachimiak
Andrzej
A
Edwards
Aled M
AM
D001710:Biotin / Q000096:biosynthesis; D002265:Carboxylic Ester Hydrolases / Q000737:chemistry* / Q000378:metabolism; D020134:Catalytic Domain; D019295:Computational Biology; D018360:Crystallography, X-Ray; D004583:Electrons; D004926:Escherichia coli / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000502:physiology*; D006860:Hydrogen Bonding; D007700:Kinetics; D013058:Mass Spectrometry; D008958:Models, Molecular; D010727:Phosphoric Diester Hydrolases / Q000378:metabolism; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary
D029968:Escherichia coli Proteins; C061417:bioH protein, E coli; D001710:Biotin; D002265:Carboxylic Ester Hydrolases; D010727:Phosphoric Diester Hydrolases