This single-stranded DNA binding protein (SSB) is found in Lactococcus phage. It can stimulate RecA-mediated homologous recombination. Its structure is a variation of the typical oligonucleotide/oligosaccharide binding-fold of single-stranded DNA binding proteins [].
ThermoDBP is a single-stranded DNA-binding protein (SSB) protein of the Thermoproteales. SSB proteins are essential for the genome maintenance of all known cellular organisms. Many SSBs contain an OB fold domain, albeit with low sequence conservation, and OB fold-containing SSB proteins have been detected in all three domains of life. However, the Thermoproteales SSB protein, ThermoDBP, lacks the OB fold and binds specifically to ssDNA with low sequence specificity. Its three-dimensional structure resembles that of the Hut operon positive regulatory protein HutP [].
DNA replication of phi29 and related phages takes place via a strand displacement mechanism, a process that generates large amounts of single-stranded DNA (ssDNA). Consequently, phage-encoded ssDNA-binding proteins (SSBs) are essential proteins during phage phi29-like DNA replication. Single-stranded DNA-binding proteins (SSBs) destabilize double-stranded DNA (dsDNA) and bind without sequence specificity, but selectively and cooperatively, to single-stranded DNA (ssDNA) conferring a regular structure to it, which is recognized and exploited by a variety of enzymes involved in DNA replication, repair and recombination.Phage phi29 protein p5 is the SSB protein active during phi29 DNA replication. It protects ssDNA against nuclease degradation and greatly stimulates dNTP incorporation during phi29 DNA replication process. Binding of the SSB to ssDNA prevents non-productive binding of the viral DNA polymerase to ssDNA, and allows the release DNA polymerase molecules that are already titrated by the ssDNA. This effect would be of particular importance in phi29-like DNA replication systems, where large amounts of ssDNA are generated and SSB binding to ssDNA could favor efficient re-usage of templates [].This domain is found in phi29-like SSB proteins, homologues are found in .
This entry represents the SOCS (suppressors of cytokine signaling) box of SSB2 (SPRY domain-containing SOCS box proteins). SSB proteins contain a central SPRY domain and a C-terminal SOCS. SSB2 has been shown to interact with c-Met, the hepatocyte growth factor receptor [, ]. It also regulates inducible nitric oxide synthase (iNOS) by targeting it for proteasomal degradation []. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions [, ].
The Escherichia coli single-strand binding protein [](gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids. It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterized in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB.Primosomal replication protein N (PriB) is a specialist protein from bacteria that binds single-stranded DNA at the primosome assembly site (PAS). The primosome is a mobile multiprotein replication priming complex which is believe to operate on the lagging-strand template at the E. coli DNA replication fork []. The primosome consists of one monomer of PriC and DnaT, two monomers of PriA, two dimers of PriB and one hexamer of DnaB [].
This group represents single-stranded DNA-binding proteins (SSB, also known as helix-destabilising proteins and gp2.5) from bacteriophage T7. It is expressed in the late stage of lytic development, binding preferentially to single-stranded DNA and is implicated in DNA replication, formation of concatemers, recombination and repair of double-stranded breaks [, , , , ]. Together with DNA primase/helicase, promotes pairing of two homologous DNA molecules containing complementary single-stranded regions and mediates homologous DNA strand exchange []. SSB disrupts loops, hairpins and other secondary structures present on ssDNA to reduce and eliminate pausing of viral DNA polymerase at specific sites during elongation []. The C-terminal aromatic Phe and the overall acidic charge of this region are critical for its function [].
This winged helix domain is found in the DprA protein [].DprA is a new member of the recombination-mediator protein family, dedicated to natural bacterial transformation []. In Helicobacter pylori, DprA is required for natural chromosomal and plasmid transformation []. It has now been shown that DprA binds cooperatively to single-stranded DNA (ssDNA) and interacts with RecA. In the process, DprA-RecA-ssDNA filaments are produced and these filaments catalyse the homology-dependent formation of joint molecules. While the Escherichia coli SSB protein limits access of RecA to ssDNA, DprA alleviates this barrier []. DprA has a role not only in ensuring production of transformants via interaction with RecA, it is also involved in competence shut-off via interaction with ComE [].
The SOCS box was first identified in SH2-domain-containing proteins of the suppressor of cytokines signalling (SOCS) family []but was later also found in:the WSB (WD-40-repeat-containing proteins with a SOCS box) family,the SSB (SPRY domain-containing proteins with a SOCS box) family,the ASB (ankyrin-repeat-containing proteins with a SOCS box) family,and ras and ras-like GTPases [].The SOCS box found in these proteins is an about 50 amino acid C-terminal domain composed of two blocks of well-conserved residues separated by between 2 and 10 non-conserved residues []. The C-terminal conserved region is an L/P-rich sequence of unknown function, whereas the N-terminal conserved region is a consensus BC box [], which binds to the Elongin BC complex [, ]. It has been demonstrated that this association couple bound proteins to the ubiquitination or proteasomal compartments [, ].
This family of bacterial proteins includes DNA processing protein A (DprA) from Streptococcus pneumoniae and Smf, the Bacillus subtilis orthologue. DprA is a new member of the recombination-mediator protein family, dedicated to natural bacterial transformation []. In Helicobacter pylori, DprA is required for natural chromosomal and plasmid transformation []. It has now been shown that DprA binds cooperatively to single-stranded DNA (ssDNA) and interacts with RecA. In the process, DprA-RecA-ssDNA filaments are produced and these filaments catalyse the homology-dependent formation of joint molecules. While the Escherichia coli SSB protein limits access of RecA to ssDNA, DprA alleviates this barrier []. DprA has a role not only in ensuring production of transformants via interaction with RecA, it is also involved in competence shut-off via interaction with ComE [].
The SOCS box was first identified in SH2-domain-containing proteins of the suppressor of cytokines signalling (SOCS) family []but was later also found in:the WSB (WD-40-repeat-containing proteins with a SOCS box) family,the SSB (SPRY domain-containing proteins with a SOCS box) family,the ASB (ankyrin-repeat-containing proteins with a SOCS box) family,and ras and ras-like GTPases [].The SOCS box found in these proteins is an about 50 amino acid C-terminal domain composed of two blocks of well-conserved residues separated by between 2 and 10 non-conserved residues []. The C-terminal conserved region is an L/P-rich sequence of unknown function, whereas the N-terminal conserved region is a consensus BC box [], which binds to the Elongin BC complex [, ]. It has been demonstrated that this association couple bound proteins to the ubiquitination or proteasomal compartments [, ].
The Bacteriophage T4 gene 59 helicase assembly protein (Gp59) is required for recombination-dependent DNA replication and repair, which is the predominant mode of DNA replication in the late stage of T4 infection. Gp59 accelerates the loading of the T4 gene 41 helicase during DNA synthesis by the T4 replication system in vitro. This protein binds to both T4 gene 41 helicase and T4 gene 32 single-stranded DNA binding protein, and to single and double-stranded DNA [].The structure of Gp59 helicase assembly protein reveals a novel α-helical bundle fold with two domains of similar size. Surface residues are predominantly basic (pI 9.37) with clusters of acidic residues but exposed hydrophobic residues suggest sites for potential contact with DNA and with other protein molecules []. The N-terminal domain shares structural homology with the high mobility group (HMG) proteins from eukaryotic organisms and it has been suggested that it plays a role in duplex DNA binding ahead of the fork. The C-terminal domain interacts with the helicase (T4 gp41) and with SSB (single-stranded binding protein T4 gp32) [].
The Bacteriophage T4 gene 59 helicase assembly protein (Gp59) is required for recombination-dependent DNA replication and repair, which is the predominant mode of DNA replication in the late stage of T4 infection. Gp59 accelerates the loading of the T4 gene 41 helicase during DNA synthesis by the T4 replication system in vitro. This protein binds to both T4 gene 41 helicase and T4 gene 32 single-stranded DNA binding protein, and to single and double-stranded DNA [].The structure of Gp59 helicase assembly protein reveals a novel α-helical bundle fold with two domains of similar size. Surface residues are predominantly basic (pI 9.37) with clusters of acidic residues but exposed hydrophobic residues suggest sites for potential contact with DNA and with other protein molecules []. The N-terminal domain shares structural homology with the high mobility group (HMG) proteins from eukaryotic organisms and it has been suggested that it plays a role in duplex DNA binding ahead of the fork. The C-terminal domain interacts with the helicase (T4 gp41) and with SSB (single-stranded binding protein T4 gp32) [].
The Bacteriophage T4 gene 59 helicase assembly protein (Gp59) is required for recombination-dependent DNA replication and repair, which is the predominant mode of DNA replication in the late stage of T4 infection. Gp59 accelerates the loading of the T4 gene 41 helicase during DNA synthesis by the T4 replication system in vitro. This protein binds to both T4 gene 41 helicase and T4 gene 32 single-stranded DNA binding protein, and to single and double-stranded DNA [].The structure of Gp59 helicase assembly protein reveals a novel α-helical bundle fold with two domains of similar size. Surface residues are predominantly basic (pI 9.37) with clusters of acidic residues but exposed hydrophobic residues suggest sites for potential contact with DNA and with other protein molecules []. The N-terminal domain shares structural homology with the high mobility group (HMG) proteins from eukaryotic organisms and it has been suggested that it plays a role in duplex DNA binding ahead of the fork. The C-terminal domain interacts with the helicase (T4 gp41) and with SSB (single-stranded binding protein T4 gp32) [].
