3TEK

ThermoDBP: a non-canonical single-stranded DNA binding protein with a novel structure and mechanism

Summary for 3TEK

• Entry DOI: 10.2210/pdb3tek/pdb
• Descriptor: ThermoDBP-single stranded DNA binding protein (2 entities in total)
• Functional Keywords: leucine zipper, single stranded dna binding, dna binding protein
• Biological source: Thermoproteus tenax
• Total number of polymer chains: 2
• Total formula weight: 34761.32

Authors

White, M.F.,Paytubi, S.,Liu, H.,Graham, S.,McMahon, S.A.,Naismith, J.H. (deposition date: 2011-08-15, release date: 2011-11-23, Last modification date: 2024-02-28)

Primary citation

Paytubi, S.,McMahon, S.A.,Graham, S.,Liu, H.,Botting, C.H.,Makarova, K.S.,Koonin, E.V.,Naismith, J.H.,White, M.F.
Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales.
Proc.Natl.Acad.Sci.USA, 109:E398-E405, 2012

PubMed Abstract: ssDNA-binding proteins (SSBs) based on the oligonucleotide-binding fold are considered ubiquitous in nature and play a central role in many DNA transactions including replication, recombination, and repair. We demonstrate that the Thermoproteales, a clade of hyperthermophilic Crenarchaea, lack a canonical SSB. Instead, they encode a distinct ssDNA-binding protein that we term "ThermoDBP," exemplified by the protein Ttx1576 from Thermoproteus tenax. ThermoDBP binds specifically to ssDNA with low sequence specificity. The crystal structure of Ttx1576 reveals a unique fold and a mechanism for ssDNA binding, consisting of an extended cleft lined with hydrophobic phenylalanine residues and flanked by basic amino acids. Two ssDNA-binding domains are linked by a coiled-coil leucine zipper. ThermoDBP appears to have displaced the canonical SSB during the diversification of the Thermoproteales, a highly unusual example of the loss of a "ubiquitous" protein during evolution.

PubMed: 22106294
DOI: 10.1073/pnas.1113277108

Experimental method

X-RAY DIFFRACTION (2 Å)