The Roles of Tryptophans in Primer Synthesis by the DNA Primase of Bacteriophage T7

Zhang, Huidong; Lee, Seung-Joo; Richardson, Charles C.

doi:10.1074/jbc.m112.366096

Cited by 10 publications

(6 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Previous reports have also revealed that tyrosine/tryptophan substitutions can have significant effects on the function nucleic acid binding proteins 15 16 . In the human DNA repair enzyme alkyl-adenine DNA glycosylase (AAG) tyrosine/tryptophan substitution mutants in the base-binding site maintain the same nucleic acid binding affinity but dramatically affect the rate constants for nucleotide flipping in and out of the active site 15 .…”

Section: Discussionmentioning

confidence: 97%

“…Although tryptophan/tyrosine substitution is considered a relatively conservative change 14 , some reports have demonstrated that tryptophan to tyrosine mutations can have large effects on the proteins function 15 16 . In order to determine the effect of tryptophan/tyrosine substitutions of PC4 orthologous proteins, we have determined the crystal structures of the DNA complexes of the PC4 W89Y mutant and MoSub1 and analysed the effect of the W89Y mutation of PC4 on DNA binding affinity.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Substitution of tryptophan 89 with tyrosine switches the DNA binding mode of PC4

Huang

Zhao

Liu

et al. 2015

Sci Rep

View full text Add to dashboard Cite

PC4, a well-known general transcription cofactor, has multiple functions in transcription and DNA repair. Residue W89, is engaged in stacking interactions with DNA in PC4, but substituted by tyrosine in some PC4 orthologous proteins. In order to understand the consequences and reveal the molecular details of this substitution we have determined the crystal structures of the PC4 orthologue MoSub1 and a PC4 W89Y mutant in complex with DNA. In the structure of MoSub1-DNA complex, Y74 interacts directly with a single nucleotide of oligo DNA. By comparison, the equivalent residue, W89 in wild type PC4 interacts with two nucleotides and the base of the second nucleotide has distinct orientation relative to that of the first one. A hydrophobic patch around W89 that favours interaction with two nucleotides is not formed in the PC4 W89Y mutant. Therefore, the change of the surface hydrophobicity around residue 89 results in a difference between the modes of DNA interaction. These results indicate that the conserved Y74 in MoSub1 or W89 in PC4, are not only key residues in making specific interactions with DNA but also required to determine the DNA binding mode of PC4 proteins.

show abstract

Section: Discussionmentioning

confidence: 97%

mentioning

confidence: 99%

Substitution of tryptophan 89 with tyrosine switches the DNA binding mode of PC4

Huang

Zhao

Liu

et al. 2015

Sci Rep

View full text Add to dashboard Cite

show abstract

“…[9] The C-terminal tail of the gp4 helicase interacts with the front basic patch (Fbp) and the TBD basic patch (TBDbp)o ft he DNA polymerase (gp5/trx), whereas the non-tail region of gp4 also interacts with gp5/trx. [11] The gp2.5 ssDNA-binding protein coats ssDNA to remove its secondary structures and also physically interacts with gp5/trx. [11] The gp2.5 ssDNA-binding protein coats ssDNA to remove its secondary structures and also physically interacts with gp5/trx.…”

Section: Introductionmentioning

confidence: 99%

“…[9][10] The primasedomain of gp4 synthesizes RNA primers to initiate lagging-strand DNA synthesis. [11] The gp2.5 ssDNA-binding protein coats ssDNA to remove its secondary structures and also physically interacts with gp5/trx. [12] These protein interactions main-…”

Section: Introductionmentioning

confidence: 99%

Protein Interactions in the T7 DNA Replisome Facilitate DNA Damage Bypass

et al. 2018

Self Cite

View full text Add to dashboard Cite

The DNA replisome inevitably encounters DNA damage during DNA replication. The T7 DNA replisome contains a DNA polymerase (gp5), the processivity factor thioredoxin (trx), a helicase-primase (gp4), and a ssDNA-binding protein (gp2.5). T7 protein interactions mediate this DNA replication. However, whether the protein interactions could promote DNA damage bypass is still little addressed. In this study, we investigated strand-displacement DNA synthesis past 8-oxoG or O -MeG lesions at the synthetic DNA fork by the T7 DNA replisome. DNA damage does not obviously affect the binding affinities between helicase, polymerase, and DNA fork. Relative to unmodified G, both 8-oxoG and O -MeG-as well as GC-rich template sequence clusters-inhibit strand-displacement DNA synthesis and produce partial extension products. Relative to the gp4 ΔC-tail, gp4 promotes DNA damage bypass. The presence of gp2.5 also promotes it. Thus, the interactions of polymerase with helicase and ssDNA-binding protein facilitate DNA damage bypass. Accessory proteins in other complicated DNA replisomes also facilitate bypassing DNA damage in similar manner. This work provides new mechanistic information relating to DNA damage bypass by the DNA replisome.

show abstract

“…In addition, it is also essential to the production of niacin. 7,8 Therefore, the determination of these three molecules is a subject of great importance not only in the eld of biomedical chemistry and neurochemistry but also for diagnostic and pathological research.…”

Section: Introductionmentioning

confidence: 99%

A simple and novel strategy for the simultaneous determination of dopamine, acetamidophenol and tryptophan based on poly(new coccine) film modified carbon paste electrode

et al. 2013

View full text Add to dashboard Cite

A polymerized film of new coccine was deposited on a carbon paste electrode (CPE) by an electropolymerization technique. Electrochemical characterization of the modified electrode was investigated by electrochemical impedance spectroscopy (EIS), cyclic voltammetry (CV) and differential pulse voltammetry (DPV). The poly(new coccine) modified CPE exhibited excellent electrocatalytic activity towards the oxidation of dopamine (DA), acetaminophenol (AP) and tryptophan (Trp) simultaneously. Well defined and separated oxidation peaks were observed by CV. Linear calibration plots for the oxidation of DA, AP and Trp were obtained in the range of 0.7-200 mM for DA, 1.5-120 mM for AP, and 0.6-50 mM for Trp. Detection limits of DA, AP and Trp were found to be 0.2, 0.3 and 0.2 mM, respectively. With good selectivity and sensitivity, the present method has been successfully applied to the determination of DA, AP and Trp in pharmaceutical samples.

show abstract

The Roles of Tryptophans in Primer Synthesis by the DNA Primase of Bacteriophage T7

Cited by 10 publications

References 34 publications

Substitution of tryptophan 89 with tyrosine switches the DNA binding mode of PC4

Substitution of tryptophan 89 with tyrosine switches the DNA binding mode of PC4

Protein Interactions in the T7 DNA Replisome Facilitate DNA Damage Bypass

A simple and novel strategy for the simultaneous determination of dopamine, acetamidophenol and tryptophan based on poly(new coccine) film modified carbon paste electrode

Contact Info

Product

Resources

About