2FDO

Crystal Structure of the Conserved Protein of Unknown Function AF2331 from Archaeoglobus fulgidus DSM 4304 Reveals a New Type of Alpha/Beta Fold

Summary for 2FDO

• Entry DOI: 10.2210/pdb2fdo/pdb
• Descriptor: Hypothetical protein AF2331 (2 entities in total)
• Functional Keywords: x-ray crystallography; multiwavelength anomalous dispersion; conserved hypothetical protein; archaeoglobus fulgidus; new type of alpha/beta fold, structural genomics, psi, protein structure initiative, midwest center for structural genomics, mcsg, unknown function
• Biological source: Archaeoglobus fulgidus
• Total number of polymer chains: 2
• Total formula weight: 21829.35

Authors

Wang, S.,Kirillova, O.,Chruszcz, M.,Cymborowski, M.T.,Skarina, T.,Gorodichtchenskaia, E.,Savchenko, A.,Edwards, A.M.,Joachimiak, A.,Minor, W.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2005-12-14, release date: 2006-01-31, Last modification date: 2022-04-13)

Primary citation

Wang, S.,Kirillova, O.,Chruszcz, M.,Gront, D.,Zimmerman, M.D.,Cymborowski, M.T.,Shumilin, I.A.,Skarina, T.,Gorodichtchenskaia, E.,Savchenko, A.,Edwards, A.M.,Minor, W.
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.
Protein Sci., 18:2410-2419, 2009

PubMed 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.

PubMed: 19768810
DOI: 10.1002/pro.251

Experimental method

X-RAY DIFFRACTION (2.4 Å)