Crystal structure of a type II dehydroquinate dehydratase-like protein from Bifidobacterium longum

Abstract

Dehydroquinate dehydratase (DHQD) catalyzes the third step in the biosynthetic shikimate pathway. Here we identify a Bifidobacterium longum protein with high sequence homology to type II DHQDs but no detectable DHQD activity under standard assay conditions. A crystal structure reveals that the B. longum protein adopts a DHQD-like tertiary structure but a distinct quaternary state. Apparently forming a dimer, the B. longum protein lacks the active site aspartic acid contributed from a neighboring protomer in the type II DHQD dodecamer. Relating to the absence of protein-protein interactions established in the type II DHQD dodecameric assembly, substantial conformational changes distinguish the would-be active site of the B. longum protein. As B. longum possess no other genes with homology to known DHQDs, these findings imply a unique DHQD activity within B. longum.

Fig. 1

Crystal structure of the DHQD-like protein from B. longum. a The M. tuberculosis type II DHQD (PDB code 2DHQ) dodecamer (a tetramer of trimers) is shown in surface representation. The three protomers that make up one trimer are colored beige, orange, and yellow. Two additional trimers visible in this perspective are colored gray and green. b The two protomers within the B. longum DHQDlike crystallographic asymmetric unit are colored green and cyan. c Superposition of the two protomers within the B. longum DHQD-like asymmetric unit on two trimers from the M. tuberculosis DHQD dodecamer. Each protomer within the M. tuberculosis trimers is colored a different shade of gray. The overlaid protomers are depicted in ribbon and the non-overlaid protomers in surface representation. Arrows denote the M. tuberculosis DHQD twofold (which coincides with the B. longum DHQD-like dimer interface) and threefold interfaces. d A superposition of protomer A of the B. longum DHQDlike (cyan) to the M. tuberculosis type II DHQD reaction product bound complex (PDB code 2DHQ, brown) is shown in stereo. Active site residues within the M. tuberculosis enzyme are represented as sticks, with corresponding residues in the B. longum protein numbered (several are disordered and thus not shown). The reaction product, dehydroshikimate (DHS), within the M. tuberculosis structure is colored yellow and the aspartic acid contributed by a neighboring molecule within the type II trimer is colored pink

Fig. 2

Sequence alignment of the DHQD-like protein from B. longum to 4 dodecameric type II DHQDs. The sequence alignment was prepared using ClustalW2. The B. longum DHQD-like secondary structure elements are depicted above the alignment. Residues that are conservatively substituted (red lettering, white background) or strictly conserved (white lettering, red background) are boxed. Type II DHQD active site residues are marked below the alignment by orange circles. Note that the aspartic acid (Asp87) that contributes to the active site of a neighboring protomer in the DHQD dodecamer is conserved in the B. longum enzyme