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RAD50, an SMC family member with multiple roles in DNA break repair: how does ATP affect function?

Kinoshita E, van der Linden E, Sanchez H, Wyman C - Chromosome Res. (2009)

Bottom Line: All current evidence indicates that ATP binding and hydrolysis cause architectural rearrangements in SMC protein complexes that are important for their functions in organizing DNA.In the case of the MRN complex, the functional significance of ATP binding and hydrolysis are not yet defined.We present some speculation on the role of ATP for function of the MRN complex based on the similarities and differences in the molecular architecture of the Rad50-containing complexes and the SMC complexes condensin and cohesin.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell Biology and Genetics, Erasmus University Medical Center, Box 2040, 3000 CA Rotterdam, The Netherlands.

ABSTRACT
The protein complex including Mre11, Rad50, and Nbs1 (MRN) functions in DNA double-strand break repair to recognize and process DNA ends as well as signal for cell cycle arrest. Amino acid sequence similarity and overall architecture make Rad50 a member of the structural maintenance of chromosome (SMC) protein family. Like SMC proteins, Rad50 function depends on ATP binding and hydrolysis. All current evidence indicates that ATP binding and hydrolysis cause architectural rearrangements in SMC protein complexes that are important for their functions in organizing DNA. In the case of the MRN complex, the functional significance of ATP binding and hydrolysis are not yet defined. Here we review the data on the ATP-dependent activities of MRN and their possible mechanistic significance. We present some speculation on the role of ATP for function of the MRN complex based on the similarities and differences in the molecular architecture of the Rad50-containing complexes and the SMC complexes condensin and cohesin.

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Comparison of the molecular architecture of SMC proteins (generalized for condensin and cohesin) and Rad50. a The arrangement of protein domains in cohesin/condensin and Rad50 monomers. The N- and C-terminal amino acid domains are juxtaposed at one end of an intramolecular coiled coil. This constitutes an ATPase head domain. The apex of the coiled coil where it folds back on itself is a globular dimerization domain for condensin and cohesin called the hinge. For Rad50 the coiled-coil apex is a smaller CxxC amino acid motif, called the hook; b The arrangement of SMC and Rad50 proteins in dimers. For condensin and cohesin, two elongated monomers are held together by a stable dimer interface between hinge domains. For Rad50 complexes, an Mre11 dimer binds two elongated Rad50 monomers, holding them together by interaction along the coiled coils near the ATPase heads; c Additional interactions among complex components. ATP binding occurs at the interface of two ATPase monomers. In this simplified cartoon for condensin and cohesin, this results in joining of the coiled coils at both ends, forming a large protein ring. Rad50 complexes are held together by Mre11 but can additionally interact at the coiled-coil apexes. Two CxxC hook domains can coordinate a zinc ion and cause a similar large protein ring to form. However, if DNA is bound at the globular ATPase/Mre11 end of the complex, the arrangement of the coiled coils changes so that they no longer interact with each other within the same complex
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Figure 2: Comparison of the molecular architecture of SMC proteins (generalized for condensin and cohesin) and Rad50. a The arrangement of protein domains in cohesin/condensin and Rad50 monomers. The N- and C-terminal amino acid domains are juxtaposed at one end of an intramolecular coiled coil. This constitutes an ATPase head domain. The apex of the coiled coil where it folds back on itself is a globular dimerization domain for condensin and cohesin called the hinge. For Rad50 the coiled-coil apex is a smaller CxxC amino acid motif, called the hook; b The arrangement of SMC and Rad50 proteins in dimers. For condensin and cohesin, two elongated monomers are held together by a stable dimer interface between hinge domains. For Rad50 complexes, an Mre11 dimer binds two elongated Rad50 monomers, holding them together by interaction along the coiled coils near the ATPase heads; c Additional interactions among complex components. ATP binding occurs at the interface of two ATPase monomers. In this simplified cartoon for condensin and cohesin, this results in joining of the coiled coils at both ends, forming a large protein ring. Rad50 complexes are held together by Mre11 but can additionally interact at the coiled-coil apexes. Two CxxC hook domains can coordinate a zinc ion and cause a similar large protein ring to form. However, if DNA is bound at the globular ATPase/Mre11 end of the complex, the arrangement of the coiled coils changes so that they no longer interact with each other within the same complex

Mentions: Rad50 resembles the SMC proteins involved in chromosome cohesion and chromatin condensation (Aravind et al. 1999; Strunnikov and Jessberger 1999). SMC proteins all contain Walker A and B nucleotide (NTP)-binding motifs at their amino- and carboxy-terminal ends, respectively. These motifs are separated by long stretches of amino acids that form an extended coiled-coil structure. The coiled coils fold back on themselves to form intramolecular association of the ATPase domains at one end and a so-called hook or hinge domain at the other end of an elongated structure (Fig. 2a). These structural elements and their architectural arrangement are exploited for various functions of Rad50 and related proteins. The core Rad50 complex is a heterotetramer of Mre11 and Rad50 (M2R2) arranged such that the DNA-binding sites on the Mre11 dimer are close to the two Rad50 ATPase domains (Fig. 2b) (de Jager et al. 2001b; Hopfner et al. 2001). The Mre11/Rad50 (MR) coiled coils are notably flexible (de Jager et al. 2001b; van Noort et al. 2003; Moreno-Herrero et al. 2005). RM binds to DNA via the globular domain with the coiled coils protruding (de Jager et al. 2001b). DNA is an allosteric effector of the RMN complex as binding DNA induces reorientation of the RAD50 coiled coils to become parallel to one another favoring the inter-complex interactions needed for DNA tethering and organizing DNA for eventual repair (Fig. 2c) (Moreno-Herrero et al. 2005).


RAD50, an SMC family member with multiple roles in DNA break repair: how does ATP affect function?

Kinoshita E, van der Linden E, Sanchez H, Wyman C - Chromosome Res. (2009)

Comparison of the molecular architecture of SMC proteins (generalized for condensin and cohesin) and Rad50. a The arrangement of protein domains in cohesin/condensin and Rad50 monomers. The N- and C-terminal amino acid domains are juxtaposed at one end of an intramolecular coiled coil. This constitutes an ATPase head domain. The apex of the coiled coil where it folds back on itself is a globular dimerization domain for condensin and cohesin called the hinge. For Rad50 the coiled-coil apex is a smaller CxxC amino acid motif, called the hook; b The arrangement of SMC and Rad50 proteins in dimers. For condensin and cohesin, two elongated monomers are held together by a stable dimer interface between hinge domains. For Rad50 complexes, an Mre11 dimer binds two elongated Rad50 monomers, holding them together by interaction along the coiled coils near the ATPase heads; c Additional interactions among complex components. ATP binding occurs at the interface of two ATPase monomers. In this simplified cartoon for condensin and cohesin, this results in joining of the coiled coils at both ends, forming a large protein ring. Rad50 complexes are held together by Mre11 but can additionally interact at the coiled-coil apexes. Two CxxC hook domains can coordinate a zinc ion and cause a similar large protein ring to form. However, if DNA is bound at the globular ATPase/Mre11 end of the complex, the arrangement of the coiled coils changes so that they no longer interact with each other within the same complex
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494100&req=5

Figure 2: Comparison of the molecular architecture of SMC proteins (generalized for condensin and cohesin) and Rad50. a The arrangement of protein domains in cohesin/condensin and Rad50 monomers. The N- and C-terminal amino acid domains are juxtaposed at one end of an intramolecular coiled coil. This constitutes an ATPase head domain. The apex of the coiled coil where it folds back on itself is a globular dimerization domain for condensin and cohesin called the hinge. For Rad50 the coiled-coil apex is a smaller CxxC amino acid motif, called the hook; b The arrangement of SMC and Rad50 proteins in dimers. For condensin and cohesin, two elongated monomers are held together by a stable dimer interface between hinge domains. For Rad50 complexes, an Mre11 dimer binds two elongated Rad50 monomers, holding them together by interaction along the coiled coils near the ATPase heads; c Additional interactions among complex components. ATP binding occurs at the interface of two ATPase monomers. In this simplified cartoon for condensin and cohesin, this results in joining of the coiled coils at both ends, forming a large protein ring. Rad50 complexes are held together by Mre11 but can additionally interact at the coiled-coil apexes. Two CxxC hook domains can coordinate a zinc ion and cause a similar large protein ring to form. However, if DNA is bound at the globular ATPase/Mre11 end of the complex, the arrangement of the coiled coils changes so that they no longer interact with each other within the same complex
Mentions: Rad50 resembles the SMC proteins involved in chromosome cohesion and chromatin condensation (Aravind et al. 1999; Strunnikov and Jessberger 1999). SMC proteins all contain Walker A and B nucleotide (NTP)-binding motifs at their amino- and carboxy-terminal ends, respectively. These motifs are separated by long stretches of amino acids that form an extended coiled-coil structure. The coiled coils fold back on themselves to form intramolecular association of the ATPase domains at one end and a so-called hook or hinge domain at the other end of an elongated structure (Fig. 2a). These structural elements and their architectural arrangement are exploited for various functions of Rad50 and related proteins. The core Rad50 complex is a heterotetramer of Mre11 and Rad50 (M2R2) arranged such that the DNA-binding sites on the Mre11 dimer are close to the two Rad50 ATPase domains (Fig. 2b) (de Jager et al. 2001b; Hopfner et al. 2001). The Mre11/Rad50 (MR) coiled coils are notably flexible (de Jager et al. 2001b; van Noort et al. 2003; Moreno-Herrero et al. 2005). RM binds to DNA via the globular domain with the coiled coils protruding (de Jager et al. 2001b). DNA is an allosteric effector of the RMN complex as binding DNA induces reorientation of the RAD50 coiled coils to become parallel to one another favoring the inter-complex interactions needed for DNA tethering and organizing DNA for eventual repair (Fig. 2c) (Moreno-Herrero et al. 2005).

Bottom Line: All current evidence indicates that ATP binding and hydrolysis cause architectural rearrangements in SMC protein complexes that are important for their functions in organizing DNA.In the case of the MRN complex, the functional significance of ATP binding and hydrolysis are not yet defined.We present some speculation on the role of ATP for function of the MRN complex based on the similarities and differences in the molecular architecture of the Rad50-containing complexes and the SMC complexes condensin and cohesin.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell Biology and Genetics, Erasmus University Medical Center, Box 2040, 3000 CA Rotterdam, The Netherlands.

ABSTRACT
The protein complex including Mre11, Rad50, and Nbs1 (MRN) functions in DNA double-strand break repair to recognize and process DNA ends as well as signal for cell cycle arrest. Amino acid sequence similarity and overall architecture make Rad50 a member of the structural maintenance of chromosome (SMC) protein family. Like SMC proteins, Rad50 function depends on ATP binding and hydrolysis. All current evidence indicates that ATP binding and hydrolysis cause architectural rearrangements in SMC protein complexes that are important for their functions in organizing DNA. In the case of the MRN complex, the functional significance of ATP binding and hydrolysis are not yet defined. Here we review the data on the ATP-dependent activities of MRN and their possible mechanistic significance. We present some speculation on the role of ATP for function of the MRN complex based on the similarities and differences in the molecular architecture of the Rad50-containing complexes and the SMC complexes condensin and cohesin.

Show MeSH