Structural view of a non Pfam singleton and crystal packing analysis.

PloS One
Chongyun ChengZhi-Jie Liu

Abstract

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. The protein crystallized in 4 different space groups that diffracted X-rays to 2.37 Å (P3(1)21), 2.17 Å (P2(1)2(1)2(1)), 3.01 Å (P4(1)22), and 2.03 Å (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° 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 α-helical protein with a central hydrophobic core providing thermal stability via π:cation and π: π interactions. A ProFunc analysis retrieved a very low match with a splicing endonuclease, sugge...Continue Reading

References

Jun 10, 1997·Proceedings of the National Academy of Sciences of the United States of America·P F KosaP B Sigler
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Aug 25, 2000·Molecular and Cellular Biology·W V SoM Rosbash
Sep 22, 2001·Acta Crystallographica. Section D, Biological Crystallography·A PerrakisV S Lamzin
Oct 24, 2002·Acta Crystallographica. Section D, Biological Crystallography·Paul D AdamsThomas C Terwilliger
Oct 4, 2003·Genome Research·Tomislav Domazet-Loso, Diethard Tautz
Oct 28, 2003·Proteins·Björn WallnerArne Elofsson
Mar 3, 2004·Acta Crystallographica. Section D, Biological Crystallography·Laurent C StoroniRandy J Read
Jun 25, 2004·Nucleic Acids Research·David E KimDavid Baker
Jun 25, 2004·Nucleic Acids Research·Ian W DavisDavid C Richardson
Sep 1, 1994·Acta Crystallographica. Section D, Biological Crystallography·UNKNOWN Collaborative Computational Project, Number 4
May 1, 1997·Acta Crystallographica. Section D, Biological Crystallography·G N MurshudovE J Dodson
Dec 2, 2004·Acta Crystallographica. Section D, Biological Crystallography·Paul Emsley, Kevin Cowtan
Dec 21, 2004·Nucleic Acids Research·Catherine BrooksbankJanet Thornton
Jan 27, 2005·The Journal of Experimental Biology·Byron BartonJim O Vigoreaux
May 5, 2005·PLoS Biology·Rasmus NielsenMichele Cargill
Oct 6, 2005·PLoS Biology·Ana Claudia MarquesHenrik Kaessmann
May 13, 2006·Science·Song XueHong Li
Aug 8, 2006·Genomics·Kohji OkamuraStephen W Scherer
Aug 8, 2007·Journal of Molecular Biology·Evgeny Krissinel, Kim Henrick
Sep 4, 2007·Journal of Structural and Functional Genomics·Dong Hae ShinSung-Hou Kim
Dec 25, 2007·Acta Crystallographica. Section A, Foundations of Crystallography·George M Sheldrick
Jan 22, 2008·BMC Genomics·Yanbin Yin, Daniel Fischer
Jan 25, 2008·BMC Bioinformatics·Yang Zhang
Jun 14, 2008·Genome Research·Qi ZhouWen Wang
Dec 10, 2008·Molecular Biology and Evolution·Macarena Toll-RieraM Mar Albà
Feb 28, 2009·Nature Protocols·Lawrence A Kelley, Michael J E Sternberg
Aug 1, 2007·Journal of Applied Crystallography·Airlie J McCoyRandy J Read
Jun 2, 2009·Nucleic Acids Research·Kevin Karplus
Nov 3, 2009·BMC Bioinformatics·Chih-Chieh ChenJinn-Moon Yang
Nov 26, 2009·Nucleic Acids Research·Catherine BrooksbankJanet Thornton
Dec 1, 2009·Journal of Molecular Biology·Diana Ekman, Arne Elofsson
Oct 5, 2010·Current Protein & Peptide Science·Sandhya R Shenoy, B Jayaram
Oct 15, 2010·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Anna E Speers, Benjamin F Cravatt
Oct 15, 2010·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Abhinav KumarAshley Deacon
Nov 13, 2010·Nucleic Acids Research·Dennis A BensonEric W Sayers
Jan 1, 1997·Methods in Enzymology·Zbyszek Otwinowski, Wladek Minor

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Methods Mentioned

BETA
gel filtration
size exclusion chromatography
PISA
protein crystal diffraction

Software Mentioned

Refmac
BLAST
/ Warp
ClustalW
Se
WuBlast
Phaser
BLOSUM62
SHELX
Jalview

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