Literature summary for 3.6.4.B7 extracted from

Chen, L.T.; Ko, T.P.; Chang, Y.W.; Lin, K.A.; Wang, A.H.; Wang, T.F.
Structural and functional analyses of five conserved positively charged residues in the L1 and N-terminal DNA binding motifs of archaeal RADA protein (2007), PLoS One, 2, e858.

Crystallization (Commentary)

Crystallization (Comment)	Organism
crystallized using the hanging drop vapor diffusion method, crystal structure of Sulfolobus solfataricus RadA overwound right-handed filament with three monomers per helical pitch. This structure reveals conformational details of the first ssDNA binding disordered loop (denoted L1 motif) and the dsDNA binding N-terminal domain (NTD). L1 and NTD together form an outwardly open palm structure on the outer surface of the helical filament. Inside this palm structure, five conserved basic amino acid residues (K27, K60, R117, R223 and R229) surround a 25 A pocket that is wide enough to accommodate anionic ssDNA, dsDNA or both. These five positively charged residues are essential for DNA binding and for RadA-catalyzed D-loop formation	Saccharolobus solfataricus

Crystallization (Comment)

Organism

crystallized using the hanging drop vapor diffusion method, crystal structure of Sulfolobus solfataricus RadA overwound right-handed filament with three monomers per helical pitch. This structure reveals conformational details of the first ssDNA binding disordered loop (denoted L1 motif) and the dsDNA binding N-terminal domain (NTD). L1 and NTD together form an outwardly open palm structure on the outer surface of the helical filament. Inside this palm structure, five conserved basic amino acid residues (K27, K60, R117, R223 and R229) surround a 25 A pocket that is wide enough to accommodate anionic ssDNA, dsDNA or both. These five positively charged residues are essential for DNA binding and for RadA-catalyzed D-loop formation

Saccharolobus solfataricus

Protein Variants

Protein Variants	Comment	Organism
K27A	mutant does not produced a D-loop product as compared to that of the wild type SsoRadA protein, 90100% reduction of the surface plasmon resonance binding signal, exhibits weaker affinity to dsDNA as compared to wild-type protein	Saccharolobus solfataricus
K27A	mutant does not produced a D-loop product as compared to that of the wild type SsoRadA protein, mutant exhibits slower ssDNA association rate	Saccharolobus solfataricus
K27R	mutant does not produced a D-loop product as compared to that of the wild type SsoRadA protein, exhibits weaker affinity to dsDNA as compared to wild-type protein	Saccharolobus solfataricus
K60A	mutant does not produced a D-loop product as compared to that of the wild type SsoRadA protein	Saccharolobus solfataricus
K60A	mutant does not produced a D-loop product as compared to that of the wild type SsoRadA protein, mutants is defective in dsDNA binding	Saccharolobus solfataricus
K60R	mutant does not produced a D-loop product as compared to that of the wild type SsoRadA protein, binds dsDNA as well as wild-type protein	Saccharolobus solfataricus
R217A	mutant does not produced a D-loop product as compared to that of the wild type SsoRadA protein, association and dissociation kinetics largely identical or similar to that of the wild-type protein, exhibits weaker affinity to dsDNA as compared to wild-type protein	Saccharolobus solfataricus
R217K	mutant does not produced a D-loop product as compared to that of the wild type SsoRadA protein, mutant exhibits slower ssDNA association rate, surface plasmon resonance binding signals is similar to that of wild-type protein, exhibits weaker affinity to dsDNA as compared to wild-type protein	Saccharolobus solfataricus
R223A	mutant does not produced a D-loop product as compared to that of the wild type SsoRadA protein, association and dissociation kinetics largely identical or similar to that of the wild-type protein, 90100% reduction of the surface plasmon resonance binding signal, mutants is defective in dsDNA binding	Saccharolobus solfataricus
R223K	mutant does not produced a D-loop product as compared to that of the wild type SsoRadA protein, surface plasmon resonance binding signals is similar to that of wild-type protein, mutants is defective in dsDNA binding	Saccharolobus solfataricus
R229A	mutant does not produced a D-loop product as compared to that of the wild type SsoRadA protein, association and dissociation kinetics largely identical or similar to that of the wild-type protein, 90100% reduction of the surface plasmon resonance binding signal, mutants is defective in dsDNA binding	Saccharolobus solfataricus
R229K	mutant does not produced a D-loop product as compared to that of the wild type SsoRadA protein, surface plasmon resonance binding signals is similar to that of wild-type protein, mutants is defective in dsDNA binding	Saccharolobus solfataricus

Organism

Organism	UniProt	Comment	Textmining
Saccharolobus solfataricus	Q55075	-	-

Synonyms

Synonyms	Comment	Organism
RadA	-	Saccharolobus solfataricus
SSO0250	locus name	Saccharolobus solfataricus