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Crystal structure and functional assignment of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12
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Rea, Dean, Hovington, Rebecca, Rakus, John F., Gerlt, John A., Fülöp, Vilmos, Bugg, Tim and Roper, David I. (2008) Crystal structure and functional assignment of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12. Biochemistry, Vol.47 (No.38). pp. 9955-9965. doi:10.1021/bi800943g ISSN 0006-2960.
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Official URL: http://dx.doi.org/10.1021/bi800943g
Abstract
One of the major challenges in the postgenomic era is the functional assignment of proteins using sequence- and structure-based predictive methods coupled with experimental validation. We have used these approaches to investigate the structure and function of the Escherichia coli K-12 protein YfaU, annotated as a putative 4-hydroxy-2-ketoheptane-1,7-dioate aldolase (HpcH) in the sequence databases. HpcH is the final enzyme in the degradation pathway of the aromatic compound homoprotocatechuate. We have determined the crystal structure of apo-YfaU and the Mg2+-pyruvate product complex. Despite greater sequence and structural similarity to HpcH, genomic context suggests YfaU is instead a 2-keto-3-deoxy sugar aldolase like the homologous 2-dehydro-3-deoxygalactarate aldolase (DDGA). Enzyme kinetic measurements show activity with the probable physiological substrate 2-keto-3-deoXy-L-rhamnonate, supporting the functional assignment, as well as the structurally similar 2-keto-3-deoxy-L-mannonate and 2-keto-3-deoxy-L-lyxonate (see accompanying paper: Rakus, J. F., Fedorov, A. A., Fedorov, E. V., Glasner, M. E., Hubbard, B. K., Delli, J. D., Babbitt, P. C., Almo, S. C., and Gerit, J. A. (2008) Biochemistry 47, 9944-9954). YfaU has similar activity toward the HpcH substrate 4-hydroxy-2-ketoheptane-1,7-dioate and synthetic substrates 4-hydroxy-2-ketopentanoic acid and 4-hydroxy-2-ketohexanoic acid. This indicates a relaxed substrate specificity that complicates the functional assignment of members of this enzyme superfamily. Crystal structures suggest these enzymes use an Asp-His intersubunit dyad to activate a metal-bound water or hydroxide for proton transfer during catalysis.
Item Type: | Journal Article | ||||
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Subjects: | Q Science > QD Chemistry Q Science > QH Natural history > QH426 Genetics Q Science > QR Microbiology |
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) > Biological Sciences ( -2010) Faculty of Science, Engineering and Medicine > Science > Chemistry |
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Library of Congress Subject Headings (LCSH): | Escherichia coli, Crystallography, Genomics, Metal ions | ||||
Journal or Publication Title: | Biochemistry | ||||
Publisher: | American Chemical Society | ||||
ISSN: | 0006-2960 | ||||
Official Date: | 23 September 2008 | ||||
Dates: |
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Volume: | Vol.47 | ||||
Number: | No.38 | ||||
Number of Pages: | 11 | ||||
Page Range: | pp. 9955-9965 | ||||
DOI: | 10.1021/bi800943g | ||||
Status: | Peer Reviewed | ||||
Publication Status: | Published | ||||
Access rights to Published version: | Restricted or Subscription Access | ||||
Funder: | Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC) | ||||
Grant number: | BBC0044501 (BBSRC) |
Data sourced from Thomson Reuters' Web of Knowledge
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