Effects of Deletion and Site-Directed Mutations on Ligation Steps of NAD+-Dependent DNA Ligase:  A Biochemical Analysis of BRCA1 C-Terminal Domain†

Biochemistry ◽  
2004 ◽  
Vol 43 (39) ◽  
pp. 12648-12659 ◽  
Author(s):  
Hong Feng ◽  
Jeremy M. Parker ◽  
Jing Lu ◽  
Weiguo Cao
Keyword(s):  
Biochemical Analysis ◽  
Dna Ligase ◽  
Terminal Domain

scholarly journals The ligation of pol β mismatch insertion products governs the formation of promutagenic base excision DNA repair intermediates

2020 ◽  
Vol 48 (7) ◽  
pp. 3708-3721 ◽  
Author(s):  
Melike Çağlayan
Keyword(s):  
Excision Repair ◽  
Dna Ligase ◽  
Active Site Residues ◽  
Dna Ligases ◽  
Terminal Domain ◽  
Dna Ligase I ◽  
Nucleotide Insertion ◽  
Base Excision ◽  
Ligation Step

Abstract DNA ligase I and DNA ligase III/XRCC1 complex catalyze the ultimate ligation step following DNA polymerase (pol) β nucleotide insertion during base excision repair (BER). Pol β Asn279 and Arg283 are the critical active site residues for the differentiation of an incoming nucleotide and a template base and the N-terminal domain of DNA ligase I mediates its interaction with pol β. Here, we show inefficient ligation of pol β insertion products with mismatched or damaged nucleotides, with the exception of a Watson–Crick-like dGTP insertion opposite T, using BER DNA ligases in vitro. Moreover, pol β N279A and R283A mutants deter the ligation of the promutagenic repair intermediates and the presence of N-terminal domain of DNA ligase I in a coupled reaction governs the channeling of the pol β insertion products. Our results demonstrate that the BER DNA ligases are compromised by subtle changes in all 12 possible noncanonical base pairs at the 3′-end of the nicked repair intermediate. These findings contribute to understanding of how the identity of the mismatch affects the substrate channeling of the repair pathway and the mechanism underlying the coordination between pol β and DNA ligase at the final ligation step to maintain the BER efficiency.

Dual functions of the N-terminal domain of S. pombe DNA ligase I

2000 ◽  
Vol 28 (5) ◽  
pp. A251-A251
Author(s):  
I. V. Martin ◽  
S. A. MacNeill
Keyword(s):  
Dna Ligase ◽  
Terminal Domain ◽  
Dna Ligase I ◽  
Dual Functions

scholarly journals Biochemical analysis of the N-terminal domain of human RAD54B

2008 ◽  
Vol 36 (17) ◽  
pp. 5441-5450 ◽  
Author(s):  
N. Sarai ◽  
W. Kagawa ◽  
N. Fujikawa ◽  
K. Saito ◽  
J. Hikiba ◽  
...  
Keyword(s):  
Biochemical Analysis ◽  
Terminal Domain

scholarly journals Biochemical analysis of human PIF1 helicase and functions of its N-terminal domain

2008 ◽  
Vol 36 (19) ◽  
pp. 6295-6308 ◽  
Author(s):  
Yongqing Gu ◽  
Yuji Masuda ◽  
Kenji Kamiya
Keyword(s):  
Biochemical Analysis ◽  
Terminal Domain ◽  
Pif1 Helicase

scholarly journals Insights into EB1 structure and the role of its C-terminal domain for discriminating microtubule tips from the lattice

2011 ◽  
Vol 22 (16) ◽  
pp. 2912-2923 ◽  
Author(s):  
Rubén M. Buey ◽  
Renu Mohan ◽  
Kris Leslie ◽  
Thomas Walzthoeni ◽  
John H. Missimer ◽  
...  
Keyword(s):  
Biochemical Analysis ◽  
Binding Proteins ◽  
Coiled Coil ◽  
Actin Binding ◽  
Terminal Domain ◽  
X Ray Scattering ◽  
C Terminus ◽  
Stable Association ◽  
Chemical Cross Linking

End-binding proteins (EBs) comprise a conserved family of microtubule plus end–tracking proteins. The concerted action of calponin homology (CH), linker, and C-terminal domains of EBs is important for their autonomous microtubule tip tracking, regulation of microtubule dynamics, and recruitment of numerous partners to microtubule ends. Here we report the detailed structural and biochemical analysis of mammalian EBs. Small-angle X-ray scattering, electron microscopy, and chemical cross-linking in combination with mass spectrometry indicate that EBs are elongated molecules with two interacting CH domains, an arrangement reminiscent of that seen in other microtubule- and actin-binding proteins. Removal of the negatively charged C-terminal tail did not affect the overall conformation of EBs; however, it increased the dwell times of EBs on the microtubule lattice in microtubule tip–tracking reconstitution experiments. An even more stable association with the microtubule lattice was observed when the entire negatively charged C-terminal domain of EBs was replaced by a neutral coiled-coil motif. In contrast, the interaction of EBs with growing microtubule tips was not significantly affected by these C-terminal domain mutations. Our data indicate that long-range electrostatic repulsive interactions between the C-terminus and the microtubule lattice drive the specificity of EBs for growing microtubule ends.

scholarly journals Biochemical and functional characterization of a meiosis-specific Pch2/ORC AAA+ assembly

2020 ◽  
Vol 3 (11) ◽  
pp. e201900630
Author(s):  
María Ascensión Villar-Fernández ◽  
Richard Cardoso da Silva ◽  
Magdalena Firlej ◽  
Dongqing Pan ◽  
Elisabeth Weir ◽  
...  
Keyword(s):  
Biochemical Analysis ◽  
Budding Yeast ◽  
Functional Characterization ◽  
Efficient Removal ◽  
Terminal Domain ◽  
Origins Of Replication ◽  
Mcm Helicase ◽  
A Subunit ◽  
Aaa Protein

Pch2 is a meiosis-specific AAA+ protein that controls several important chromosomal processes. We previously demonstrated that Orc1, a subunit of the ORC, functionally interacts with budding yeast Pch2. The ORC (Orc1-6) AAA+ complex loads the AAA+ MCM helicase to origins of replication, but whether and how ORC collaborates with Pch2 remains unclear. Here, we show that a Pch2 hexamer directly associates with ORC during the meiotic G2/prophase. Biochemical analysis suggests that Pch2 uses its non-enzymatic NH2-terminal domain and AAA+ core and likely engages the interface of ORC that also binds to Cdc6, a factor crucial for ORC-MCM binding. Canonical ORC function requires association with origins, but we show here that despite causing efficient removal of Orc1 from origins, nuclear depletion of Orc2 and Orc5 does not trigger Pch2/Orc1-like meiotic phenotypes. This suggests that the function for Orc1/Pch2 in meiosis can be executed without efficient association of ORC with origins of replication. In conclusion, we uncover distinct functionalities for Orc1/ORC that drive the establishment of a non-canonical, meiosis-specific AAA+ assembly with Pch2.

scholarly journals Functional and Biochemical Analysis of the N-terminal Domain of Phytochrome A

2006 ◽  
Vol 281 (45) ◽  
pp. 34421-34429 ◽  
Author(s):  
Julieta L. Mateos ◽  
Juan Pablo Luppi ◽  
Ouliana B. Ogorodnikova ◽  
Vitaly A. Sineshchekov ◽  
Marcelo J. Yanovsky ◽  
...  
Keyword(s):  
Biochemical Analysis ◽  
Phytochrome A ◽  
Terminal Domain

scholarly journals The C-terminal domain of yeast PCNA is required for physical and functional interactions with Cdc9 DNA ligase

2007 ◽  
Vol 35 (5) ◽  
pp. 1624-1637 ◽  
Author(s):  
Sangeetha Vijayakumar ◽  
Brian R. Chapados ◽  
Kristina H. Schmidt ◽  
Richard D. Kolodner ◽  
John A. Tainer ◽  
...  
Keyword(s):  
Dna Ligase ◽  
Functional Interactions ◽  
Terminal Domain
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