HHsearch alignment for GI: 254780709 and conserved domain: TIGR00606

>TIGR00606 rad50 rad50; InterPro: IPR004584 Rad50 is involved in recombination, recombinational repair, and/or non-homologous end joining. It is a component of an exonuclease complex with MRE11 homologs. The Saccharomyces cerevisiae Rad50/MRE11 complex possesses single-stranded endonuclease activity and ATP-dependent double-strand-specific exonuclease activity. Rad50 provides an ATP-dependent control of MRE11 by unwinding and repositioning DNA ends into the MRE11 active site. This family is distantly related to the SbcC family of bacterial proteins. When the N- and C-terminal globular regions of Rad50 from Pyrococcus furiosus P58301 from SWISSPROT are co-expressed in Escherichia coli, they spontaneously associate to form a stable complex that possesses ATP-binding and weak ATP-hydrolysing activities. The structure formed is known as the Rad50 catalytic domain (Rad50cd1). In the presence of ATP, two Rad50cd1 molecules interact via their ATP-binding and highly conserved 'signature' motifs to form a dimer. As ATP is buried deep within this dimer interface, the two Rad50cd1 molecules may have to completely disengage after ATP hydrolysis to allow the release of ADP before binding of a new ATP molecule. ATP binding is also accompanied by a 30 rotation of two distinct domains within each Rad50cd1 part of the dimer. This rotation and dimerisation creates a positively charged surface which, potentially, could provide a DNA-binding site capable of accommodating two DNA molecules. The Mre11-docking site within Rad50 has been mapped to two 40-residue heptad-repeat sequences that lie adjacent to the N- and C-terminal ATPase segments. A distinct region within this domain forms a conserved hydrophobic patch that is believed to be the actual Mre11-binding site and lies immediately adjacent to the putative DNA-binding site of Rad50. As Rad50 dimerises in the presence of ATP and forms a stoichiometric complex with Mre11 (one Mre11 subunit binding to one Rad50 subunit), it is possible that the MR complex forms a closely coordinated DNA-binding unit that has the potential to act on two DNA molecules simultaneously. Within this unit, ATP-dependent control of nuclease action might be achieved via Rad50 unwinding or repositioning DNA ends into the active-site of Mre11 . ; GO: 0005524 ATP binding, 0006281 DNA repair, 0030870 Mre11 complex.
Probab=96.10  E-value=0.002  Score=44.33  Aligned_cols=20  Identities=55%  Similarity=0.758  Sum_probs=10.8

Q ss_pred             ECCCCCCCCHHHHHHHHHHH
Q ss_conf             11354444424789999999
Q gi|254780709|r  115 LVVGVNGVGKTTVIGKLSKK  134 (321)
Q Consensus       115 l~vG~nG~GKTTT~aKLA~~  134 (321)
T Consensus        32 ~l~GPNG~GKTT~IE~L~y~   51 (1328)
T TIGR00606        32 LLVGPNGAGKTTIIEALKYV   51 (1328)
T ss_pred             EEECCCCCCHHHHHHHHHHH
T ss_conf             01277887525898754332