2VWT

Crystal structure of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12 - Mg-pyruvate product complex

Summary for 2VWT

• Entry DOI: 10.2210/pdb2vwt/pdb
• Related: 2VWS
• Descriptor: YFAU, 2-KETO-3-DEOXY SUGAR ALDOLASE, MAGNESIUM ION, PYRUVIC ACID, ... (6 entities in total)
• Functional Keywords: lyase, (beta/alpha)8 barrel, 2-keto-3-deoxy sugar aldolase, escherichia coli k-12 protein yfau, degradation of homoprotocatechuate, pyruvate, class ii aldolase
• Biological source: ESCHERICHIA COLI
• Total number of polymer chains: 3
• Total formula weight: 87542.94

Authors

Rea, D.,Rakus, J.F.,Gerlt, J.A.,Fulop, V.,Bugg, T.D.H.,Roper, D.I. (deposition date: 2008-06-26, release date: 2008-09-09, Last modification date: 2023-12-13)

Primary citation

Rea, D.,Hovington, R.,Rakus, J.F.,Gerlt, J.A.,Fulop, V.,Bugg, T.D.H.,Roper, D.I.
Crystal Structure and Functional Assignment of Yfau, a Metal Ion Dependent Class II Aldolase from Escherichia Coli K12.
Biochemistry, 47:9955-, 2008

PubMed 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 Mg (2+)-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 Gerlt, 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.

PubMed: 18754683
DOI: 10.1021/BI800943G

Experimental method

X-RAY DIFFRACTION (1.93 Å)