Rad50 zinc hook functions as a constitutive dimerization module interchangeable with SMC hinge

Abstract

The human Mre11/Rad50 complex is one of the key factors in genome maintenance pathways. Previous nanoscale imaging by atomic force microscopy (AFM) showed that the ringlike structure of the human Mre11/Rad50 complex transiently opens at the zinc hook of Rad50. However, imaging of the human Mre11/Rad50 complex by high-speed AFM shows that the Rad50 coiled-coil arms are consistently bridged by the dimerized hooks while the Mre11/Rad50 ring opens by disconnecting the head domains; resembling other SMC proteins such as cohesin or condensin. These architectural features are conserved in the yeast and bacterial Mre11/Rad50 complexes. Yeast strains harboring the chimeric Mre11/Rad50 complex containing the SMC hinge of bacterial condensin MukB instead of the RAD50 hook properly functions in DNA repair. We propose that the basic role of the Rad50 hook is similar to that of the SMC hinge, which serves as rather stable dimerization interface.

A Disease-Causing Single Amino Acid Deletion in the Coiled-Coil Domain of RAD50 Impairs MRE11 Complex Functions in Yeast and Humans

“…The coiled-coil structure, which is conserved across the SMC proteins and all known Rad50 orthologs ( de Jager et al., 2004 ; Paull, 2018 ; Stracker and Petrini, 2011 ; Syed and Tainer, 2018 ), comprises a heptad repeat pattern wherein the first and the fourth residues are hydrophobic to allow the association of antiparallel helices via their hydrophobic faces ( de Jager et al., 2001 ; Truebestein and Leonard, 2016 ; van Noort et al., 2003 ). The apex of the RAD50 coiled coil consists of a zinc (Zn)-hook domain by which two MRE11-RAD50 complexes can dimerize to form intra- and intermolecular complexes that have been proposed to bridge DNA ends ( Hohl et al., 2015 ; Hopfner, 2014 ; Park et al., 2017 ; Paull, 2018 ; Stracker and Petrini, 2011 ; Syed and Tainer, 2018 ; Tatebe et al., 2020 ). It has also been recently suggested that MRE11-RAD50 complexes could promote DNA tethering of sister chromatids at stalled forks by facilitating Cohesin loading ( Delamarre et al., 2020 ).…”

“…Although the flexibility of the RAD50 coiled-coil domain has prevented determination of its whole structure at atomic resolution ( Käshammer et al., 2019 ; Park et al., 2017 ), several studies suggested that this domain participates in the regulation of MRN functions by propagating information from the Zn-hook domain to the globular domain ( Hohl et al., 2011 , 2015 ; Park et al., 2017 ). Analyses using crystallographic microscopy, cryo-electron microscopy (cryo-EM), and high-throughput single-molecule microscopy suggested that dimers of the ATP-bound MRE11-RAD50 intracomplex (M 2 R 2 ) mostly adopt a ring conformation that can interact and scan the DNA homoduplex to recognize the DNA end and trigger ATM/Tel1-dependent DDR ( Deshpande et al., 2014 ; Hopfner, 2014 ; Käshammer et al., 2019 ; Myler et al., 2017 ; Tatebe et al., 2020 ). A model suggested that upon ATP and DNA binding, the MRE11-RAD50 intracomplex undergoes a conformational switch, leading to the interaction of intermolecular coiled-coil domains and resulting in a rod-shaped structure.…”

Mutation Spectra of the MRN (MRE11, RAD50, NBS1/NBN) Break Sensor in Cancer Cells

“…The position in the middle of the protein where the two coiled-coil domains fold on themselves is characterized by a zinc hook domain. This zinc hook domain also facilitates dimerization of the RAD50 protein [ 29 , 78 , 79 ]. Our analysis of COSMIC mutations revealed a hotspot frameshift mutation within the Zn finger domain (K722Rfs*14) [ 75 , 80 , 81 , 82 ] ( Figure 4 ).…”

Atomic force microscopy—A tool for structural and translational DNA research

“… 186 High-speed AFM was used to determine the global architecture of these human, yeast, and bacterial complexes including the impact of the Nbs1 subunit on the human MRN complex. 187 Tatebe and colleagues 187 showed that the ring structure of Mre11/Rad50 repeats an open-close action at the head, but the hook between the Rad50 dimer remains closed. They demonstrated that the global architecture and conformational features of the Mre11/Rad50 complex were conserved.…”