3UT8: Structural View Of A Non Pfam Singleton And Crystal Packing Analysis

BACKGROUND: Comparative genomic analysis has revealed that in each genome a large number of open reading frames have no homologues in other species. Such singleton genes have attracted the attention of biochemists and structural biologists as a potential untapped source of new folds. Cthe_2751 is a 15.8 kDa singleton from an anaerobic, hyperthermophile Clostridium thermocellum. To gain insights into the architecture of the protein and obtain clues about its function, we decided to solve the structure of Cthe_2751. RESULTS: The protein crystallized in 4 different space groups that diffracted X-rays to 2.37 A (P3(1)21), 2.17 A (P2(1)2(1)2(1)), 3.01 A (P4(1)22), and 2.03 A (C222(1)) resolution, respectively. Crystal packing analysis revealed that the 3-D packing of Cthe_2751 dimers in P4(1)22 and C222(1) is similar with only a rotational difference of 2.69 degrees around the C axes. A new method developed to quantify the differences in packing of dimers in crystals from different space groups corroborated the findings of crystal packing analysis. Cthe_2751 is an all alpha-helical protein with a central hydrophobic core providing thermal stability via pi:cation and pi: pi interactions. A ProFunc analysis retrieved a very low match with a splicing endonuclease, suggesting a role for the protein in the processing of nucleic acids. CONCLUSIONS: Non-Pfam singleton Cthe_2751 folds into a known all alpha-helical fold. The structure has increased sequence coverage of non-Pfam proteins such that more protein sequences can be amenable to modelling. Our work on crystal packing analysis provides a new method to analyze dimers of the protein crystallized in different space groups. The utility of such an analysis can be expanded to oligomeric structures of other proteins, especially receptors and signaling molecules, many of which are known to function as oligomers.
PDB ID: 3UT8Download
MMDB ID: 98363
PDB Deposition Date: 2011/11/25
Updated in MMDB: 2012/03
Experimental Method:
x-ray diffraction
Resolution: 2.17  Å
Source Organism:
Similar Structures:
Biological Unit for 3UT8: dimeric; determined by author and by software (PISA)
Molecular Components in 3UT8
Label Count Molecule
Proteins (2 molecules)
Putative Uncharacterized Protein
Molecule annotation
Chemicals (5 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB