3N8B

Crystal Structure of Borrelia burgdorferi Pur-alpha

Summary for 3N8B

• Entry DOI: 10.2210/pdb3n8b/pdb
• Related: 3K44
• Descriptor: Uncharacterized protein, 1,2-ETHANEDIOL, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: pur-alpha, pur repeat, pur domain, whirly fold, rna binding, dna binding, nucleic acid binding protein
• Biological source: Borrelia burgdorferi (Lyme disease spirochete)
• Total number of polymer chains: 2
• Total formula weight: 23335.46

Authors

Graebsch, A.,Roche, S.,Kostrewa, D.,Niessing, D. (deposition date: 2010-05-28, release date: 2010-10-06, Last modification date: 2024-10-09)

Primary citation

Graebsch, A.,Roche, S.,Kostrewa, D.,Soding, J.,Niessing, D.
Of bits and bugs--on the use of bioinformatics and a bacterial crystal structure to solve a eukaryotic repeat-protein structure.
Plos One, 5:e13402-e13402, 2010

PubMed Abstract: Pur-α is a nucleic acid-binding protein involved in cell cycle control, transcription, and neuronal function. Initially no prediction of the three-dimensional structure of Pur-α was possible. However, recently we solved the X-ray structure of Pur-α from the fruitfly Drosophila melanogaster and showed that it contains a so-called PUR domain. Here we explain how we exploited bioinformatics tools in combination with X-ray structure determination of a bacterial homolog to obtain diffracting crystals and the high-resolution structure of Drosophila Pur-α. First, we used sensitive methods for remote-homology detection to find three repetitive regions in Pur-α. We realized that our lack of understanding how these repeats interact to form a globular domain was a major problem for crystallization and structure determination. With our information on the repeat motifs we then identified a distant bacterial homolog that contains only one repeat. We determined the bacterial crystal structure and found that two of the repeats interact to form a globular domain. Based on this bacterial structure, we calculated a computational model of the eukaryotic protein. The model allowed us to design a crystallizable fragment and to determine the structure of Drosophila Pur-α. Key for success was the fact that single repeats of the bacterial protein self-assembled into a globular domain, instructing us on the number and boundaries of repeats to be included for crystallization trials with the eukaryotic protein. This study demonstrates that the simpler structural domain arrangement of a distant prokaryotic protein can guide the design of eukaryotic crystallization constructs. Since many eukaryotic proteins contain multiple repeats or repeating domains, this approach might be instructive for structural studies of a range of proteins.

PubMed: 20976240
DOI: 10.1371/journal.pone.0013402

Experimental method

X-RAY DIFFRACTION (1.9 Å)