Single stranded binding protein: Difference between revisions

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Phe-60 is an important DNA binding site. It has been shown to be the site for cross-linking.
Phe-60 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  
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
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  
DNA,  whereas modification of either lysine residues (with acetic anhydride) or tryptophan  
residues (with N-bromosuccinimide) led to complete loss of binding activity” ( Meyer, 348).  
residues (with N-bromosuccinimide) led to complete loss of binding activity ( Meyer, 348).  
The two tryptophan residues involved in DNA binding are Try-40 and Try-54, which was  
The two tryptophan residues involved in DNA binding are Trp40 and Trp54, which was  
determined by mutagenesis. One more binding site was determined by site-specific mutagenesis.
determined by mutagenesis. One more binding site was determined by site-specific mutagenesis.
When His-55 is substituted with Leu it decreases binding affinity. All of these residues  
When His55 is substituted with Leu it decreases binding affinity. All of these residues  
are found in a hydrophobic region, which is suitable for nucleotide base interactions.
are found in a hydrophobic region, which is suitable for nucleotide base interactions.


Line 30: Line 30:
===SSB-Protein Interactions===
===SSB-Protein Interactions===


It is believed that Gly-15 may play an important role in binding the RecA protein. Mutations in Gly-15 have  
It is believed that Gly15 may play an important role in binding the RecA protein. Mutations in Gly15 have  
extreme effects on recombinational repair.  SSB has also been thought to bind with exonuclease I, DNA polymerase II,  
extreme effects on recombinational repair.  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.  
and a protein n, which is used to help synthesize RNA primers for the lagging strand.  

Revision as of 18:02, 1 November 2013

Sandbox Single Stranded DNA-Binding Protein (SSB)Sandbox Single Stranded DNA-Binding Protein (SSB)


Introduction

The single stranded DNA binding protein (SSB) of E. coli plays an important role in three aspects of DNA metabolism – namely in replication, repair and recombination. During DNA replication, SSB molecules bind to the newly separated DNA strands, keeping the strands separated by holding them in place so that each strand can serve as a template.


Structure

SSB consists is a homotetramer that has a DNA binding domain which binds to a single strand of DNA. The tetramers consist of α-helices, β-sheets, and random coils.


Structure of Single Stranded DNA-Binding Protein bound to ssDNA (PDB entry 1eyg)

Drag the structure with the mouse to rotate

Binding Interactions in the Active SiteBinding Interactions in the Active Site

Phe-60 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 ( Meyer, 348). The two tryptophan residues involved in DNA binding are Trp40 and Trp54, which was determined by mutagenesis. One more binding site was determined by site-specific mutagenesis. When His55 is substituted with Leu it decreases binding affinity. All of these residues are found in a hydrophobic region, which is suitable for nucleotide base interactions.


SSB-Protein Interactions

It is believed that Gly15 may play an important role in binding the RecA protein. Mutations in Gly15 have

extreme effects on recombinational repair. 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.

Structure of Single Stranded DNA-Binding Protein bound to ssDNA (PDB entry 2vw9)

Drag the structure with the mouse to rotate

See AlsoSee Also

ReferencesReferences


PMID: 2087220

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

Refayat Ahsen, Rachel Craig, Alexander Berchansky, Michal Harel
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