The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of α + β fold

The structure of AF2331, a 11‐kDa orphan protein of unknown function from Archaeoglobus fulgidus, was solved by Se‐Met MAD to 2.4 Å resolution. The structure consists of an α + β fold formed by an unusual homodimer, where the two core β‐sheets are interdigitated, containing strands alternating from both subunits. The decrease in solvent‐accessible surface area upon dimerization is unusually large (3960 Ų) for a protein of its size. The percentage of the total surface area buried in the interface (41.1%) is one of the largest observed in a nonredundant set of homodimers in the PDB and is above the mean for nearly all other types of homo‐oligomers. AF2331 has no sequence homologs, and no structure similar to AF2331 could be found in the PDB using the CE, TM‐align, DALI, or SSM packages. The protein has been identified in Pfam 23.0 as the archetype of a new superfamily and is topologically dissimilar to all other proteins with the “3‐Layer (BBA) Sandwich” fold in CATH. Therefore, we propose that AF2331 forms a novel α + β fold. AF2331 contains multiple negatively charged surface clusters and is located on the same operon as the basic protein AF2330. We hypothesize that AF2331 and AF2330 may form a charge‐stabilized complex in vivo, though the role of the negatively charged surface clusters is not clear.