scholarly journals Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism

2021 ◽  
Author(s):  
Alfonso Mondragon ◽  
Amy Osterman
Keyword(s):  
Dna Repair ◽  
Dna Binding ◽  
Conformational Change ◽  
Active Site ◽  
Binding Mode ◽  
Relaxation Mechanism ◽  
Processivity Factor ◽  
Ap Lyase ◽  
The Way

Topoisomerase V is a unique topoisomerase that combines DNA repair and topoisomerase activities. The enzyme has an unusual arrangement, with a small topoisomerase domain followed by 12 tandem (HhH)2 domains, which include three AP lyase repair domains. The unusual architecture of this enzyme bears no resemblance to any other known topoisomerase. Here we present structures of topoisomerase V in complex with DNA. The structures show that the (HhH)2 domains wrap around the DNA and in this manner appear to act as a processivity factor. There is a conformational change in the protein to expose the topoisomerase active site. The DNA bends sharply to enter the active site, which melts the DNA and probably facilitates relaxation. The structures show a DNA binding mode not observed before and provide information on the way this unusual topoisomerase relaxes DNA.

scholarly journals DNA binding induces active site conformational change in the human TREX2 3'-exonuclease

2009 ◽  
Vol 37 (7) ◽  
pp. 2411-2417 ◽  
Author(s):  
U. de Silva ◽  
F. W. Perrino ◽  
T. Hollis
Keyword(s):  
Dna Binding ◽  
Conformational Change ◽  
Active Site

Two-step mechanism involving active-site conformational changes regulates human telomerase DNA binding

2015 ◽  
Vol 465 (2) ◽  
pp. 347-357 ◽  
Author(s):  
Christopher G. Tomlinson ◽  
Aaron L. Moye ◽  
Jessica K. Holien ◽  
Michael W. Parker ◽  
Scott B. Cohen ◽  
...  
Keyword(s):  
Dna Binding ◽  
Reverse Transcriptase ◽  
Conformational Change ◽  
Conformational Changes ◽  
Active Site ◽  
Reverse Transcriptase Domain ◽  
Human Telomerase ◽  
Initial Binding ◽  
Dna Substrate ◽  
Step Mechanism

Initial binding of the enzyme telomerase to its DNA substrate proceeds by a two-step mechanism involving enzyme conformational change. A protein loop in the reverse transcriptase domain is involved in these conformational changes.

scholarly journals Identification of residues in the human DNA repair enzyme HAP1 (Ref-1) that are essential for redox regulation of Jun DNA binding.

1993 ◽  
Vol 13 (9) ◽  
pp. 5370-5376 ◽  
Author(s):  
L J Walker ◽  
C N Robson ◽  
E Black ◽  
D Gillespie ◽  
I D Hickson
Keyword(s):  
Dna Repair ◽  
Dna Binding ◽  
Active Site ◽  
Cysteine Residue ◽  
Binding Activity ◽  
Repair Enzyme ◽  
Exonuclease Iii ◽  
Terminal Domain ◽  
Dna Binding Activity ◽  
Redox Active

The DNA binding activity of the c-jun proto-oncogene product is inhibited by oxidation of a specific cysteine residue (Cys-252) in the DNA binding domain. Jun protein inactivated by oxidation of this residue can be efficiently reactivated by a factor from human cell nuclei, recently identified as a DNA repair enzyme (termed HAP1 or Ref-1). The HAP1 protein consists of a core domain, which is highly conserved in a family of prokaryotic and eukaryotic DNA repair enzymes, and a 61-amino-acid N-terminal domain absent from bacterial homologs such as Escherichia coli exonuclease III. The eukaryote-specific N-terminal domain was dispensable for the DNA repair functions of the HAP1 protein but was essential for reactivation of the DNA binding activity of oxidized Jun protein. Consistent with this finding, exonuclease III protein could not reactive Jun. A minimal 26-residue region of the N-terminal domain proximal to the core of the HAP1 enzyme was required for redox activity. By site-directed mutagenesis, cysteine 65 was identified as the redox active site in the HAP1 enzyme. In addition, it is proposed that cysteine 93 interacts with the redox active site, probably via disulfide bridge formation. It is concluded that the HAP1 protein has evolved a novel redox activation domain capable of regulating the DNA binding activity of a proto-oncogene product which is not essential for its DNA repair functions. Identification of a putative active site cysteine residue should facilitate analysis of the mechanism by which the HAP1 protein may alter the redox state of a wide range of transcription factors.

Identification of residues in the human DNA repair enzyme HAP1 (Ref-1) that are essential for redox regulation of Jun DNA binding

1993 ◽  
Vol 13 (9) ◽  
pp. 5370-5376
Author(s):  
L J Walker ◽  
C N Robson ◽  
E Black ◽  
D Gillespie ◽  
I D Hickson
Keyword(s):  
Dna Repair ◽  
Dna Binding ◽  
Active Site ◽  
Cysteine Residue ◽  
Binding Activity ◽  
Repair Enzyme ◽  
Exonuclease Iii ◽  
Terminal Domain ◽  
Dna Binding Activity ◽  
Redox Active

The DNA binding activity of the c-jun proto-oncogene product is inhibited by oxidation of a specific cysteine residue (Cys-252) in the DNA binding domain. Jun protein inactivated by oxidation of this residue can be efficiently reactivated by a factor from human cell nuclei, recently identified as a DNA repair enzyme (termed HAP1 or Ref-1). The HAP1 protein consists of a core domain, which is highly conserved in a family of prokaryotic and eukaryotic DNA repair enzymes, and a 61-amino-acid N-terminal domain absent from bacterial homologs such as Escherichia coli exonuclease III. The eukaryote-specific N-terminal domain was dispensable for the DNA repair functions of the HAP1 protein but was essential for reactivation of the DNA binding activity of oxidized Jun protein. Consistent with this finding, exonuclease III protein could not reactive Jun. A minimal 26-residue region of the N-terminal domain proximal to the core of the HAP1 enzyme was required for redox activity. By site-directed mutagenesis, cysteine 65 was identified as the redox active site in the HAP1 enzyme. In addition, it is proposed that cysteine 93 interacts with the redox active site, probably via disulfide bridge formation. It is concluded that the HAP1 protein has evolved a novel redox activation domain capable of regulating the DNA binding activity of a proto-oncogene product which is not essential for its DNA repair functions. Identification of a putative active site cysteine residue should facilitate analysis of the mechanism by which the HAP1 protein may alter the redox state of a wide range of transcription factors.

DNA Binding Mode of Transition Metal Complexes, A Relationship to Tumor Cell Toxicity

2014 ◽  
Vol 21 (26) ◽  
pp. 3081-3094 ◽  
Author(s):  
M. Ashfaq ◽  
T. Najam ◽  
S.S.A. Shah ◽  
M.M. Ahmad ◽  
S. Shaheen ◽  
...  
Keyword(s):  
Dna Binding ◽  
Transition Metal ◽  
Tumor Cell ◽  
Metal Complexes ◽  
Transition Metal Complexes ◽  
Binding Mode ◽  
Cell Toxicity

scholarly journals HPF1 remodels the active site of PARP1 to enable the serine ADP-ribosylation of histones

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Fa-Hui Sun ◽  
Peng Zhao ◽  
Nan Zhang ◽  
Lu-Lu Kong ◽  
Catherine C. L. Wong ◽  
...  
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Active Site ◽  
Negative Charge ◽  
Structural Data ◽  
Dna Breaks ◽  
Adp Ribosylation ◽  
Local Conformation ◽  
Key Residues ◽  
Structural Insights

AbstractUpon binding to DNA breaks, poly(ADP-ribose) polymerase 1 (PARP1) ADP-ribosylates itself and other factors to initiate DNA repair. Serine is the major residue for ADP-ribosylation upon DNA damage, which strictly depends on HPF1. Here, we report the crystal structures of human HPF1/PARP1-CAT ΔHD complex at 1.98 Å resolution, and mouse and human HPF1 at 1.71 Å and 1.57 Å resolution, respectively. Our structures and mutagenesis data confirm that the structural insights obtained in a recent HPF1/PARP2 study by Suskiewicz et al. apply to PARP1. Moreover, we quantitatively characterize the key residues necessary for HPF1/PARP1 binding. Our data show that through salt-bridging to Glu284/Asp286, Arg239 positions Glu284 to catalyze serine ADP-ribosylation, maintains the local conformation of HPF1 to limit PARP1 automodification, and facilitates HPF1/PARP1 binding by neutralizing the negative charge of Glu284. These findings, along with the high-resolution structural data, may facilitate drug discovery targeting PARP1.

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