Flexibility of the linker between the domains of DNA methyltransferase SsoII revealed by small-angle X-ray scattering: implications for transcription regulation in SsoII restriction-modification system.
(Cytosine-5)-DNA methyltransferase SsoII (M.SsoII) consists of a methyltransferase domain (residues 72-379) and an N-terminal region (residues 1-71) which regulates transcription in SsoII restriction-modification system. Small-angle X-ray scattering (SAXS) is employed here to study the low resolution structure of M.SsoII and its complex with DNA containing the methylation site. The shapes reconstructed ab initio from the SAXS data reveal two distinct protein domains of unequal size. The larger domain matches the crystallographic structure of a homologous DNA methyltransferase HhaI (M.HhaI), and the cleft in this domain is occupied by DNA in the model of the complex reconstructed from the SAXS data. This larger domain can thus be identified as the methyltransferase domain whereas the other domain represents the N-terminal region. Homology modeling of the M.SsoII structure is performed by using the model of M.HhaI for the methyltransferase domain and representing the N-terminal region either as a flexible chain of dummy residues or as a rigid structure of a homologous protein (phage 434 repressor) connected to the methyltransferase domain by a short flexible linker. Both models are compatible with the SAXS data and demonstrate high mobility of the N-terminal region. The linker flexibility might play an important role in the function of M.SsoII as a transcription factor.
European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany.
Petr V
PV
Konarev
Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia.
Galina S
GS
Kachalova
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
Alexandra Yu
AY
Ryazanova
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
Elena A
EA
Kubareva
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia; Gamaleya Institute of Epidemiology and Microbiology, Moscow, Russia; Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia.
Anna S
AS
Karyagina
Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia.
Hans D
HD
Bartunik
European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany.
Dmitri I
DI
Svergun
D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D004269:DNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D015257:DNA-Cytosine Methylases / Q000737:chemistry* / Q000378:metabolism; D017434:Protein Structure, Tertiary; D013329:Structure-Activity Relationship; D014158:Transcription, Genetic; D014961:X-Ray Diffraction
D001426:Bacterial Proteins; D004269:DNA, Bacterial; C063974:DNA modification methylase SsoII; D015257:DNA-Cytosine Methylases