The 1.7 Å crystal structure of the apo form of the soluble quinoprotein glucose dehydrogenase from Acinetobacter calcoaceticus reveals a novel internal conserved sequence repeat

Abstract

The crystal structure of a dimeric apo form of the soluble quinoprotein glucose dehydrogenase (s-GDH) from Acinetobacter calcoaceticus has been solved by multiple isomorphous replacement followed by density modification, and was subsequently refined at 1.72 Å resolution to a final crystallographic R-factor of 16.5 % and free R-factor of 0.8 %. The s-GDH monomer has a β-propeller fold consisting of six four-stranded anti-parallel β-sheets aligned around a pseudo 6-fold symmetry axis. The enzyme binds three calcium ions per monomer, two of which are located in the dimer interface. The third is bound in the putative active site, where it may bind and functionalize the pyrroloquinoline quinone (PQQ) cofactor. A data base search unexpectedly showed that four uncharacterized protein sequences are homologous to s-GDH with many residues in the putative active site absolutely conserved. This indicates that these homologs may have a similar structure and that they may catalyze similar PQQ-dependent reactions. A structure-based sequence alignment of the six four-stranded β-sheets in s-GDH’s β-propeller fold shows an internally conserved sequence repeat that gives rise to two distinct conserved structural motifs. The first structural motif is found at the corner of the short β-turn between the inner two β-strands of the β-sheets, where an Asp side-chain points back into the β-sheet to form a hydrogen-bond with the OH/NH of a Tyr/Trp side-chain in the same β-sheet. The second motif involves an Arg/Lys side-chain in the C β-strand of one β-sheet, which forms a bidentate salt-bridge with an Asp/Glu in the CD loop of the next β-sheet. These intra and inter-β-sheet hydrogen-bonds are likely to contribute to the stability of the s-GDH β-propeller fold.