Proteopedia

Single stranded binding protein: Difference between revisions

← Older editNewer edit →
No edit summary
No edit summary
Line 12: Line 12:
</StructureSection>
</StructureSection>


==Binding Interactions in the Active Site==
====Binding Interactions in the Active Site====
Single-stranded DNA can interact with SSB through hydrogen bonds, stacking, or electronegative interactions.  Though SSB proteins are found in a variety of different organisms, most interactions between SSB and ssDNA happen through the common structural motif of an oligosaccharide/oligonucleotide binding site, referred to as the OB fold <ref>Shamoo, Yousif.  “Single Stranded DNA binding proteins.” ‘’Encyclopedia of Life Sciences.’’  MacMillan Publishers Ltd, Nature Publishing Group; 2002</ref>.  The OB fold allows SSB to bind preferentially to ssDNA.  Each subunit of a SSB has an OB fold (the SSB of E. coli thus has four OB folds, one per each of its four identical subunits).  This fold consists of a 5-stranded β barrel that ends in an α-helix.   
Single-stranded DNA can interact with SSB through hydrogen bonds, stacking, or electronegative interactions.  Though SSB proteins are found in a variety of different organisms, most interactions between SSB and ssDNA happen through the common structural motif of an oligosaccharide/oligonucleotide binding site, referred to as the OB fold <ref>Shamoo, Yousif.  “Single Stranded DNA binding proteins.” ‘’Encyclopedia of Life Sciences.’’  MacMillan Publishers Ltd, Nature Publishing Group; 2002</ref>.  The OB fold allows SSB to bind preferentially to ssDNA.  Each subunit of a SSB has an OB fold (the SSB of E. coli thus has four OB folds, one per each of its four identical subunits).  This fold consists of a 5-stranded β barrel that ends in an α-helix.   


Line 19: Line 19:
One more key residue in the binding site, His55, was determined by site-specific mutagenesis, as when His55 is substituted with Leu it decreases the overall binding affinity for ssDNA.  All of these residues are found in a hydrophobic region, which is suitable for nucleotide base interactions. Treatments that modified arginine, cysteine, or tyrosine residues had no effect on binding of SSB to DNA, suggesting that these amino acids are not involved in significant interactions of the protein with the ssDNA.  
One more key residue in the binding site, His55, was determined by site-specific mutagenesis, as when His55 is substituted with Leu it decreases the overall binding affinity for ssDNA.  All of these residues are found in a hydrophobic region, which is suitable for nucleotide base interactions. Treatments that modified arginine, cysteine, or tyrosine residues had no effect on binding of SSB to DNA, suggesting that these amino acids are not involved in significant interactions of the protein with the ssDNA.  


==Interactions Between E. coli SSB and other Proteins==
====Interactions Between E. coli SSB and other Proteins====


Most of the molecule loses flexibility after ssDNA binding.  However, three phenylalanine residues (Phe147, Phe171, Phe177) in the COOH terminal domain remain flexible, even after DNA binding, suggesting that the COOH terminus has something to do with protein binding (PMID: 2087220).  An experiment where Phe177 was changed to Cys resulted in a protein that could not replicate DNA. This replication defect stemming from the lost phenylalanine residue was likely a result of the inability of the altered C-terminal region to bind other proteins necessary for replication (PMID:2453719).   
Most of the molecule loses flexibility after ssDNA binding.  However, three phenylalanine residues (Phe147, Phe171, Phe177) in the COOH terminal domain remain flexible, even after DNA binding, suggesting that the COOH terminus has something to do with protein binding (PMID: 2087220).  An experiment where Phe177 was changed to Cys resulted in a protein that could not replicate DNA. This replication defect stemming from the lost phenylalanine residue was likely a result of the inability of the altered C-terminal region to bind other proteins necessary for replication (PMID:2453719).   
Line 29: Line 29:


As single-stranded DNA binding proteins are utilized in some of the most important aspects of DNA metabolism, they are used extensively in DNA replication, repair and recombination.  Most SSBs use one or more subunits with an OB-fold motif to bind securely and preferentially to ssDNA.  A few specific SSBs (such as RecA and adenovirus DBP) do not use the OB-fold, instead relying on electrostatic and stacking interactions as well as hydrogen bonding.   
As single-stranded DNA binding proteins are utilized in some of the most important aspects of DNA metabolism, they are used extensively in DNA replication, repair and recombination.  Most SSBs use one or more subunits with an OB-fold motif to bind securely and preferentially to ssDNA.  A few specific SSBs (such as RecA and adenovirus DBP) do not use the OB-fold, instead relying on electrostatic and stacking interactions as well as hydrogen bonding.   
</StructureSection>
====Binding Interactions in the Active Site====
ssDNA can interact with binding proteins through hydrogen bonds, stacking, or electronegative interactions. Most interactions between SSB and ssDNA happen through the OB fold. OB stands for oligosaccharide/oligonucleotide binding site. This fold consists of a 5-stranded β barrel that ends in an α-helix.
<scene name='56/566528/Labeled_phe/1'>Phe56</scene> is an important DNA binding site. It has been shown to be the site for cross-linking.
Tryptophan and Lysine residues are important in binding as well. Treatments resulting in
modification of arginine, cysteine, or tyrosine residues had no effect on binding of SSB to
DNA,  whereas modification of either lysine residues (with acetic anhydride) or tryptophan
residues (with N-bromosuccinimide) led to complete loss of binding activity <ref>PMID: 2087220</ref>.
==SSB-Protein Interactions==
SSB can form complexes with many other proteins. This trait can keep enzymes needed for damage repair, transcription, etc. near the ssDNA and it is thought that SSB can even help to stimulate these enzymes to carry out their jobs. When DNA binds SSB, most of the molecule loses flexibility. But the COOH terminal domain remain flexible, even after DNA binding. It is believed that the COOH terminus has something to do with protein binding <ref>PMID: 2087220</ref>.
SSB will interact with the protein RecA to enable recombination, because RecA will recognize SSB and replace it on the strand.
In DNA repair, SSB will bind to the damaged strand to protect it. And eventually it will attract repair enzymes which will replace SSB and begin repair mechanisms.
SSB has also been thought to bind with exonuclease I, DNA polymerase II,
and a protein n, which is used to help synthesize RNA primers for the lagging strand. SSB can also help regulate transcription by competing with other proteins for binding spaces on DNA. SSB has a higher affinity for DNA than most other proteins, and those proteins are not able to remove SSB from DNA and bind themselves. This type of mechanism can not only regulate transcription, but it can provide protection for the DNA <ref>PMID: 2087220</ref>.
</StructureSection>
</StructureSection>


Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Refayat Ahsen, Rachel Craig, Alexander Berchansky, Michal Harel
Retrieved from "https://proteopedia.openfox.io/w/Single_stranded_binding_protein"