title: The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of alpha + beta fold.
abstract: The structure of AF2331, a 11-kDa orphan protein of unknown function from Archaeoglobus fulgidus, was solved by Se-Met MAD to 2.4 A resolution. The structure consists of an alpha + beta fold formed by an unusual homodimer, where the two core beta-sheets are interdigitated, containing strands alternating from both subunits. The decrease in solvent-accessible surface area upon dimerization is unusually large (3960 A(2)) 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 alpha + beta 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.
authors.affiliation: Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA.
authors.forename: Shuren
authors.initials: S
authors.lastname: Wang
authors.forename: Olga
authors.initials: O
authors.lastname: Kirillova
authors.forename: Maksymilian
authors.initials: M
authors.lastname: Chruszcz
authors.forename: Dominik
authors.initials: D
authors.lastname: Gront
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Zimmerman
authors.forename: Marcin T
authors.initials: MT
authors.lastname: Cymborowski
authors.forename: Igor A
authors.initials: IA
authors.lastname: Shumilin
authors.forename: Tatiana
authors.initials: T
authors.lastname: Skarina
authors.forename: Elena
authors.initials: E
authors.lastname: Gorodichtchenskaia
authors.forename: Alexei
authors.initials: A
authors.lastname: Savchenko
authors.forename: Aled M
authors.initials: AM
authors.lastname: Edwards
authors.forename: Wladek
authors.initials: W
authors.lastname: Minor
mesh_terms: D019843:Archaeal Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D019611:Archaeoglobus fulgidus / Q000235:genetics*; D019295:Computational Biology; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D055503:Protein Multimerization / Q000235:genetics*; D017434:Protein Structure, Tertiary / Q000235:genetics*
chemical_list: D019843:Archaeal Proteins