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Literature summary for 2.7.7.101 extracted from

  • Chilingaryan, Z.; Headey, S.J.; Lo, A.T.Y.; Xu, Z.Q.; Otting, G.; Dixon, N.E.; Scanlon, M.J.; Oakley, A.J.
    Fragment-based discovery of inhibitors of the bacterial DnaG-SSB interaction (2018), Antibiotics, 7, 14 .
    View publication on PubMedView publication on EuropePMC
Search for more literature for 2.7.7.101

Cloned(Commentary)

Cloned (Comment) Organism
recombinant expression of central and C-terminal domains of Escherichia coli DnaG primase (residues 111-581), here called DnaG-RCD, and of amino acid residues 115-581 Escherichia coli

Protein Variants

Protein Variants Comment Organism
K447A site-directed mutagenesis, the DnaGC point mutant shows dramatically attenuated SSB-Ct binding Escherichia coli
K518A site-directed mutagenesis, the DnaGC point mutant shows dramatically attenuated SSB-Ct binding Escherichia coli
R452A site-directed mutagenesis, the DnaGC point mutant shows dramatically attenuated SSB-Ct binding Escherichia coli
T450A site-directed mutagenesis, the DnaGC point mutant shows dramatically attenuated SSB-Ct binding Escherichia coli

Inhibitors

Inhibitors Comment Organism Structure
additional information STD-NMR is used to demonstrate binding of one hit to other SSB-Ct binding partners, confirming the possibility of simultaneous inhibition of multiple protein/SSB interactions. The fragment molecules represent promising scaffolds on which to build to discover antibacterial compounds, molecular docking, overview. Structures of hits with binding affinities for further optimization Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
ssDNA + n NTP Escherichia coli
-
 ssDNA/pppN(pN)n-1 hybrid + (n-1) diphosphate
-
 ?

Organism

Organism UniProt Comment Textmining
Escherichia coli P0ABS5
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
ssDNA + n NTP
-
 Escherichia coli ssDNA/pppN(pN)n-1 hybrid + (n-1) diphosphate
-
 ?

Subunits

Subunits Comment Organism
More an N-terminal zinc-binding domain (ZBD) responsible for DNA template recognition, a central catalytic domain (RNA polymerase domain, RPD), and a C-terminal helicase-binding domain (HBD or DnaGC), which is responsible for interaction with DnaB helicase and single-stranded DNA-binding protein (SSB) Escherichia coli

Synonyms

Synonyms Comment Organism
DnaG
-
 Escherichia coli
DnaG primase
-
 Escherichia coli

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.4
-
 assay at Escherichia coli

General Information

General Information Comment Organism
additional information the C-terminal hexapeptide motif of SSB (DDDIPF, SSB-Ct) is highly conserved and is known to engage in essential interactions with many proteins in nucleic acid metabolism, including primase. The SSB-Ct binding site in DnaGC has been identified by NMR. The binding pocket is formed by basic residues K447, R452, and K518, as well as T450, M451, I455, and L519. The conserved R452 residue forms a salt bridge with the carboxylic acid of the C-terminal Phe residue of the SSB-Ct, whereas the other positively charged residues around the binding pocket interact with the negatively charged residues of SSB-Ct Escherichia coli
physiological function DnaG is a DNA-dependent RNA polymerase. In bacteria, the DnaG primase is responsible for synthesis of short RNA primers used to initiate chain extension by replicative DNA polymerase(s) during chromosomal replication. Among the proteins with which Escherichia coli DnaG interacts is the single-stranded DNA-binding protein, SSB. SSB protects single-stranded DNA during DNA replication Escherichia coli