scholarly journals A Complexed Crystal Structure of a Single-Stranded DNA-Binding Protein with Quercetin and the Structural Basis of Flavonol Inhibition Specificity

2022 ◽  
Vol 23 (2) ◽  
pp. 588
Author(s):  
En-Shyh Lin ◽  
Ren-Hong Luo ◽  
Cheng-Yang Huang
Keyword(s):  
Crystal Structure ◽  
Binding Protein ◽  
Binding Activity ◽  
Structural Basis ◽  
Molecular Evidence ◽  
Mobility Shift ◽  
Single Stranded Dna ◽  
Ssdna Binding ◽  
Replacement Method ◽  
Ssdna Binding Protein

Single-stranded DNA (ssDNA)-binding protein (SSB) plays a crucial role in DNA replication, repair, and recombination as well as replication fork restarts. SSB is essential for cell survival and, thus, is an attractive target for potential antipathogen chemotherapy. Whether naturally occurring products can inhibit SSB remains unknown. In this study, the effect of the flavonols myricetin, quercetin, kaempferol, and galangin on the inhibition of Pseudomonas aeruginosa SSB (PaSSB) was investigated. Furthermore, SSB was identified as a novel quercetin-binding protein. Through an electrophoretic mobility shift analysis, myricetin could inhibit the ssDNA binding activity of PaSSB with an IC50 of 2.8 ± 0.4 μM. The effect of quercetin, kaempferol, and galangin was insignificant. To elucidate the flavonol inhibition specificity, the crystal structure of PaSSB complexed with the non-inhibitor quercetin was solved using the molecular replacement method at a resolution of 2.3 Å (PDB entry 7VUM) and compared with a structure with the inhibitor myricetin (PDB entry 5YUN). Although myricetin and quercetin bound PaSSB at a similar site, their binding poses were different. Compared with myricetin, the aromatic ring of quercetin shifted by a distance of 4.9 Å and an angle of 31o for hydrogen bonding to the side chain of Asn108 in PaSSB. In addition, myricetin occupied and interacted with the ssDNA binding sites Lys7 and Glu80 in PaSSB whereas quercetin did not. This result might explain why myricetin could, but quercetin could not, strongly inhibit PaSSB. This molecular evidence reveals the flavonol inhibition specificity and also extends the interactomes of the natural anticancer products myricetin and quercetin to include the OB-fold protein SSB.

scholarly journals Identification of the mouse low-salt-eluting single-stranded DNA-binding protein as a mammalian lactate dehydrogenase-A isoenzyme

1986 ◽  
Vol 233 (3) ◽  
pp. 913-916 ◽  
Author(s):  
F S Sharief ◽  
S H Wilson ◽  
S S-L Li
Keyword(s):  
Lactate Dehydrogenase ◽  
Binding Protein ◽  
Rabbit Antiserum ◽  
Single Stranded Dna ◽  
Ssdna Binding ◽  
Low Salt ◽  
Ssdna Binding Protein ◽  
A Subunit ◽  
Cellulose Column ◽  
Mouse Myeloma

A 36,000-Mr protein purified from mouse myeloma on the basis of selective binding to a single-stranded DNA (ssDNA)-cellulose column has been identified as the lactate dehydrogenase A (LDH-A) subunit. A homogeneous preparation of this mouse myeloma ssDNA-binding protein, termed the ‘low-salt-eluting protein’, was found to possess LDH activity, and rabbit antiserum prepared against this protein was shown to cross-react with purified 36,000-Mr LDH-A subunits from mouse and bovine sources. In addition, bovine and human LHD-A4 isoenzymes were shown to be capable of binding ssDNA. These enzymic and immunological identities with LDH-A were not observed with purified helix-destabilizing protein 1 from mouse myeloma. A model for ssDNA-LDH binding is discussed.

scholarly journals Structural basis of SOSS1 complex assembly and recognition of ssDNA

2014 ◽  
Vol 70 (a1) ◽  
pp. C844-C844
Author(s):  
Wendan Ren ◽  
Hongxia Chen ◽  
Qiangzu Sun ◽  
Xuhua Tang ◽  
Siew Choo Lim ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Double Strand Breaks ◽  
Structural Basis ◽  
Dna Double Strand Breaks ◽  
Dsb Repair ◽  
Complex Assembly ◽  
Single Stranded Dna ◽  
Strand Breaks ◽  
Ssdna Binding

The SOSS1 complex comprising SOSSA, SOSSB1 and SOSSC senses single-stranded DNA (ssDNA) and promotes repair of DNA double-strand breaks (DSBs). But how SOSS1 is assembled and recognizes ssDNA remains elusive. Crystal structure of the N-terminal half of SOSSA (SOSSAN) in complex with SOSSB1 and SOSSC showed that SOSSAN serves as a scaffold to bind both SOSSB1 and SOSSC for assembling the SOSS1 complex. The structures of SOSSAN/B1 in complex with a 12nt ssDNA and SOSSAN/B1/C in complex with a 35nt ssDNA showed that SOSSB1 interacts with both SOSSAN and ssDNA via two distinct surfaces. Recognition of ssDNA with a length up to nine nucleotides is solely mediated by SOSSB1 while neither SOSSC nor SOSSAN are critical for ssDNA binding. These results reveal the structural basis of SOSS1 assembly and provide a framework for further studying the mechanism governing longer ssDNA recognition by the SOSS1 complex during DSB repair.

scholarly journals A Phage Single-Stranded DNA (ssDNA) Binding Protein Complements ssDNA Accumulation of a Geminivirus and Interferes with Viral Movement

1999 ◽  
Vol 73 (2) ◽  
pp. 1609-1616 ◽  
Author(s):  
Malla Padidam ◽  
Roger N. Beachy ◽  
Claude M. Fauquet
Keyword(s):  
Binding Protein ◽  
Systemic Infection ◽  
Plant Viruses ◽  
Wild Type Virus ◽  
Wild Type ◽  
Direct Role ◽  
Single Stranded Dna ◽  
Ssdna Binding ◽  
Ssdna Binding Protein ◽  
Tomato Leaf Curl

ABSTRACT Geminiviruses are plant viruses with circular single-stranded DNA (ssDNA) genomes encapsidated in double icosahedral particles. Tomato leaf curl geminivirus (ToLCV) requires coat protein (CP) for the accumulation of ssDNA in protoplasts and in plants but not for systemic infection and symptom development in plants. In the absence of CP, infected protoplasts accumulate reduced levels of ssDNA and increased amounts of double-stranded DNA (dsDNA), compared to accumulation in the presence of wild-type virus. To determine whether the gene 5 protein (g5p), a ssDNA binding protein from Escherichia coli phage M13, could restore the accumulation of ssDNA, ToLCV that lacked the CP gene was modified to express g5p or g5p fused to the N-terminal 66 amino acids of CP (CP66:6G:g5). The modified viruses led to the accumulation of wild-type levels of ssDNA and high levels of dsDNA. The accumulation of ssDNA was apparently due to stable binding of g5p to viral ssDNA. The high levels of dsDNA accumulation during infections with the modified viruses suggested a direct role for CP in viral DNA replication. ToLCV that produced the CP66:6G:g5 protein did not spread efficiently in Nicotiana benthamiana plants, and inoculated plants developed only very mild symptoms. In infected protoplasts, the CP66:6G:g5 protein was immunolocalized to nuclei. We propose that the fusion protein interferes with the function of the BV1 movement protein and thereby prevents spread of the infection.

scholarly journals Insight into the dynamics of APOBEC3G protein in complexes with DNA assessed by high speed AFM

2019 ◽  
Vol 1 (10) ◽  
pp. 4016-4024 ◽  
Author(s):  
Yangang Pan ◽  
Luda S. Shlyakhtenko ◽  
Yuri L. Lyubchenko
Keyword(s):  
Reverse Transcription ◽  
Viral Genome ◽  
High Speed ◽  
Binding Protein ◽  
Single Stranded Dna ◽  
Ssdna Binding ◽  
Hiv Virus ◽  
Ssdna Binding Protein ◽  
Insight Into

APOBEC3G (A3G) is a single-stranded DNA (ssDNA) binding protein that restricts the HIV virus by deamination of dC to dU during reverse transcription of the viral genome.

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