3N2X

Crystal structure of YagE, a prophage protein belonging to the dihydrodipicolinic acid synthase family from E. coli K12 in complex with pyruvate

Summary for 3N2X

• Entry DOI: 10.2210/pdb3n2x/pdb
• Related: 2V8Z 2V9D
• Descriptor: Uncharacterized protein yagE, 1,2-ETHANEDIOL (3 entities in total)
• Functional Keywords: tim barrel, protein-ligand complex, aldolase, lyase
• Biological source: Escherichia coli
• Cellular location: Cytoplasm : P75682
• Total number of polymer chains: 4
• Total formula weight: 129003.52

Authors

Bhaskar, V.,Kumar, P.M.,Manicka, S.,Krishnaswamy, S. (deposition date: 2010-05-19, release date: 2011-04-13, Last modification date: 2023-11-29)

Primary citation

Bhaskar, V.,Kumar, M.,Manicka, S.,Tripathi, S.,Venkatraman, A.,Krishnaswamy, S.
Identification of biochemical and putative biological role of a xenolog from Escherichia coli using structural analysis.
Proteins, 79:1132-1142, 2011

PubMed Abstract: YagE is a 33 kDa prophage protein encoded by CP4-6 prophage element in Escherichia coli K12 genome. Here, we report the structures of YagE complexes with pyruvate (PDB Id 3N2X) and KDGal (2-keto-3-deoxy galactonate) (PDB Id 3NEV) at 2.2A resolution. Pyruvate depletion assay in presence of glyceraldehyde shows that YagE catalyses the aldol condensation of pyruvate and glyceraldehyde. Our results indicate that the biochemical function of YagE is that of a 2-keto-3-deoxy gluconate (KDG) aldolase. Interestingly, E. coli K12 genome lacks an intrinsic KDG aldolase. Moreover, the over-expression of YagE increases cell viability in the presence of certain bactericidal antibiotics, indicating a putative biological role of YagE as a prophage encoded virulence factor enabling the survival of bacteria in the presence of certain antibiotics. The analysis implies a possible mechanism of antibiotic resistance conferred by the over-expression of prophage encoded YagE to E. coli.

PubMed: 21294156
DOI: 10.1002/prot.22949

Experimental method

X-RAY DIFFRACTION (2.2 Å)