Why not using the gff file format. You can download them from NCBI genomes databases. There are also lots of conversion tools available to convert from GFF to BED (bedtools, galaxy, BEDOPS, ...)

use the following link http://microbes.ucsc.edu/cgi-bin/hgTables?org=Escherichia+coli+K12&db=eschColi_K12&hgsid=1455159&hgta_doMainPage=1

under output option select BED

and then select get output, select your options in next window and download your bed format for E. coli

Does anybody have the E. coli K12 GTF file with 5' and 3' UTR coordinates?

I looked at RegulonDb but it is a bit of a mess