5SYQ

Solution structure of Aquifex aeolicus Aq1974

Replaces:  2N0P

Summary for 5SYQ

• Entry DOI: 10.2210/pdb5syq/pdb
• NMR Information: BMRB: 30154
• Descriptor: Uncharacterized protein aq_1974 (1 entity in total)
• Functional Keywords: aromatic claw protein of unknown function highly aromatic protein, structural genomics, protein structure initiative, northeast structural genomics consortium, nesg, midwest center for structural genomics, mcsg, psi-biology, unknown function
• Biological source: Aquifex aeolicus (strain VF5)
• Total number of polymer chains: 1
• Total formula weight: 10415.74

Authors

Sachleben, J.R.,Gawlak, G.,Hoey, R.J.,Liu, G.,Joachimiak, A.,Montelione, G.T.,Koide, S.,Northeast Structural Genomics Consortium (NESG),Midwest Center for Structural Genomics (MCSG) (deposition date: 2016-08-11, release date: 2016-09-28, Last modification date: 2024-05-15)

Primary citation

Sachleben, J.R.,Adhikari, A.N.,Gawlak, G.,Hoey, R.J.,Liu, G.,Joachimiak, A.,Montelione, G.T.,Sosnick, T.R.,Koide, S.
Aromatic claw: A new fold with high aromatic content that evades structural prediction.
Protein Sci., 26:208-217, 2017

PubMed Abstract: We determined the NMR structure of a highly aromatic (13%) protein of unknown function, Aq1974 from Aquifex aeolicus (PDB ID: 5SYQ). The unusual sequence of this protein has a tryptophan content five times the normal (six tryptophan residues of 114 or 5.2% while the average tryptophan content is 1.0%) with the tryptophans occurring in a WXW motif. It has no detectable sequence homology with known protein structures. Although its NMR spectrum suggested that the protein was rich in β-sheet, upon resonance assignment and solution structure determination, the protein was found to be primarily α-helical with a small two-stranded β-sheet with a novel fold that we have termed an Aromatic Claw. As this fold was previously unknown and the sequence unique, we submitted the sequence to CASP10 as a target for blind structural prediction. At the end of the competition, the sequence was classified a hard template based model; the structural relationship between the template and the experimental structure was small and the predictions all failed to predict the structure. CSRosetta was found to predict the secondary structure and its packing; however, it was found that there was little correlation between CSRosetta score and the RMSD between the CSRosetta structure and the NMR determined one. This work demonstrates that even in relatively small proteins, we do not yet have the capacity to accurately predict the fold for all primary sequences. The experimental discovery of new folds helps guide the improvement of structural prediction methods.

PubMed: 27750371
DOI: 10.1002/pro.3069

Experimental method

SOLUTION NMR