Chapter 6: The Contribution of Structural Proteomics to Understanding the Function of Hypothetical Proteins
Michael D. Suits, Allan Matte, Zongchao Jia and Miroslaw Cygler [1]
Molecular Tour
Structural Genomics efforts throughout the world have led to the development of high-throughput (HTP) techniques from go from genes to 3D structures. These HTP methods have yield thousands of new structures, many of which are from hypothetical proteins, with less than 30% sequence identity to a protein of known 3D structure, and are unknown function. In order to attempt to make functional assignments for these proteins, The Montreal-Kingston Bacterial Structural Genomics Initiative
[1] has been utilizing 3D structural information of these newly determined proteins. Here are illustrations of several such examples.
A quinate/shikimate dehydrogenase from Escherichia coli - YdiB
(1o9b [2], monomer A is in magenta, monomer B is in cyan), as it possessed 28% sequence identity to E. coli AroE, a characterized shikimate dehydrogenase[3].
(1nyt). YdiB is in magenta, AroE is in yellow, carbon atoms of NAD and NADP are in green. . Both enzymes share similar folds, contain signature motifs indicative of dinucleotide (NAD+, NADP+) binding, and while AroE is a monomer, the crystal structure of E. coli YdiB revealed a dimer [2].
, as it involves a relatively , but is consistent with the molecular weight determined by size exclusion chromatography. Both enzymes consist of two α/β domains, with the C-terminal domain adopting a canonical Rossmann fold topology, consistent with dinucleotide binding.
Escherichia coli Proteins Associated With Heme Metabolism
At the initiation of our investigation ChuS, from Shigella dysenteriae, was known only as a protein up-regulated under low iron conditions, responsible for the prevention of heme toxicity. It showed low sequence homology to know 3D structures and thus there was no clear function for this protein.
, 9-stranded anti-parallel β-sheets, each flanked at its N-terminus by one pair of parallel α-helices and at its C-terminus by a set of three α-helices in an helix-loop-helix-loop-helix configuration. N- and C-terminal domains are colored red and blue, respectively. The structure clearly indicated that ChuS arose by gene duplication, as can be seen by on each other resulting in an RMS of of 2.1 Å. Based on the ChuS site directed mutation studies were carried out that indicated that demonstrate in the (N- and C-terminal domains are colored indigo and green, respectively) that . Carbon atoms of heme are in yellow, Arg100 and His193 are in magenta, and water molecules are in red. It is also interesting to note that the displays a surprising degree of similarity to the monomer structures of two other heme utilization operon proteins, E. coli ChuS and Y. enterocolitica HemS, both of which have an internal domain repeat.
