Structure of the hypothetical protein AQ_1354 from Aquifex aeolicus.

The crystal structure of a hypothetical protein AQ_1354 (gi 2983779) from the hyperthermophilic bacteria Aquifex aeolicus has been determined using X-ray crystallography. As found in many structural genomics studies, this protein is not associated with any known function based on its amino-acid sequence. PSI-BLAST analysis against a non-redundant sequence database gave 68 similar sequences referred to as 'conserved hypothetical proteins' from the uncharacterized protein family UPF0054 (accession No. PF02310). Crystallographic analysis revealed that the overall fold of this protein consists of one central alpha-helix surrounded by a four-stranded beta-sheet and four other alpha-helices. Structure-based homology analysis with DALI revealed that the structure has a moderate to good resemblance to metal-dependent proteinases such as collagenases and gelatinases, thus suggesting its possible molecular function. However, experimental tests for collagenase and gelatinase-type function show no detectable activity under standard assay conditions. Therefore, we suggest either that the members of the UPF0054 family have a similar fold but different biochemical functions to those of collagenases and gelatinases or that they have a similar function but perform it under different conditions.