PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons

Related Articles
Cas4 Nuclease and Bacterial Immunity
February 2014
Protein-Nucleic Acid Interaction: Inhibition Through Allostery
July 2013
Stabilizing DNA Single Strands
July 2013
AlkB Homologs
August 2012
Methyl maintenance
May 2012
Follow the RNA leader
December 2011
RNA Chaperone NMB1681
July 2011
Seeing HetR
July 2011
Structure from sequence
July 2011
Added benefits
April 2011
Nitrile Reductase QueF
March 2011
Inhibiting factor
February 2011
Tryptophanyl-tRNA Synthetase
February 2011
Regulating nitrogen assimilation
January 2011
Subtle shifts
January 2011
tRNA Isopentenyltransferase MiaA
August 2010
Mre11 Nuclease
May 2010
Seek and destroy 8-oxoguanine
May 2010
Antibiotics and Ribosome Function
March 2010
Pseudouridine Synthase TruA
November 2009
Get3 into the groove
October 2009
Guanine Nucleotide Exchange Factor Vav1 and Rho GTPase Rac1
October 2009
Proofreading RNA
July 2009
Hda and DNA Replication
June 2009
The elusive helicase
April 2009
Poly(A) RNA recognition
January 2009
Scavenger Decapping Enzyme DcpS
November 2008
Bacteriophage Lambda cII Protein
October 2008
RNase T
July 2008
SARS Coronavirus Nonstructural Protein 1
June 2008

Research Themes DNA and RNA

Stabilizing DNA Single Strands

SBKB [doi:10.3942/psi_sgkb/fm_2013_7]
Featured System - July 2013
Short description: PSI researchers have determined the structure of a new single-stranded DNA-binding domain, revealing a surprising connection between the kingdoms of life.

DNA is typically found in the familiar double helix, with two complementary strands interacting through base pairing. However, during many genetic processes such as transcription, repair, and recombination, the helix is unwound and the two strands are exposed. This can be a problem. Single strands have a strong tendency to fold up into local double-helical structures such as hairpins, which can inhibit these processes. Also, single DNA strands are more prone to damage by chemicals or nucleolytic enzymes. So, all known cells build specific proteins that bind to DNA single strands and protect them.

Discovering a New SSB

PSI researchers at NESG have recently discovered a new single-stranded DNA binding protein (SSB) in the bacterium Lactococcus lactis, an important industrial bacterium used in dairy fermentations. A domain from the protein YdbC was identified as an interesting target for structural genomics, and through a series of biochemical studies, it was found that it has strong, but nonspecific, affinity for single-stranded DNA, as well as weaker affinity for RNA. Attempts to crystallize the protein with single-stranded DNA have not yet been successful, but the structures of the domain alone (PDB entry 2ltd) and its complex with two short pieces of DNA (PDB entry 2ltt, shown here with DNA in orange) were determined using isotope-filtered NMR methods. The structures showed a surprising difference from the typical protein fold used to bind single DNA strands.

SSB Folds

Most single-stranded DNA binding proteins are folded with a distinctive topology, known as the OB (oligosaccharide/oligonucleotide-binding) domain. This domain forms a groove that surrounds the DNA, and is also important for oligomerization of the protein. For instance, the SSB from Escherichia coli, shown here at the bottom (PDB entry 1eyg), is composed of four protein chains, each folding into an OB domain. The single-stranded DNA wraps around the outside of the complex. The SSB in our own cells, known as replication protein A (RPA), has similar OB domains but is formed of three chains. Compare this to the YdbC DNA-binding domain, shown here at the top, which has an entirely different protein topology and is composed of two protein chains.

Structural Similarities

Looking at SSB proteins from many different organisms, we find that the DNA-binding structures are quite similar, most often forming an OB domain, but the amino acid sequences are very divergent. A similar observation was made with the fold of YdbC. Looking in the PDB, there are two other proteins with similar folds: human positive cofactor 4 (PDB entry 2c62) and Pur-alpha from fruit flies (PDB entry 3k44). However, they have very little amino acid sequence homology, so the evolutionary connection between the bacterial and the eukaryotic proteins were not apparent until the structures were solved.

Binding to DNA Single Strands

Single-stranded DNA-binding proteins bind very tightly to DNA, but with very little specificity for particular nucleotide sequences. They accomplish this by interacting strongly with the DNA backbone, through hydrogen bonds with the phosphates and riboses and complementary charge interactions with the phosphates. They also have chemically generic pockets, often lined with aromatic or hydrophobic amino acids, that surround the DNA bases but don't form specific contacts with the base-pairing surfaces. To take a closer look at these interactions in YdbC, the JSmol tab below displays an interactive JSmol.

YdbC Single-stranded DNA-binding Domain (PDB entry 2ltt)

This structure includes two protein chains (blue and green) each bound to a short single DNA strand (red). Use the buttons to highlight the positively-charged amino acids and notice their interaction with the DNA phosphates, and to highlight the aromatic and hydrophobic amino acids and notice how they form pockets for the bases.


  1. Rossi, P. et al. Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the function of protein domain family DUF2128 and expand the single-stranded DNA-binding domain proteome. Nucl. Acids Res. 41, 2756-2768 (2013).

  2. Marceau, A. H. Functions of Single-strand DNA-binding proteins in DNA replication, recombination, and repair. Meth. Mol. Biol. 922, 1-21 (2012).

  3. Raghunathan, S., Kozlov, A. G., Lohman, T. M. & Waksman, G. Structure of the DNA binding domain of E. coli SSB bound to ssDNA. Nat. Struct. Biol. 7, 648-652 (2000).

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health