Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications.
Type I restriction-modification enzymes are differentiated from type II and type III enzymes by their recognition of two specific dsDNA sequences separated by a given spacer and cleaving DNA randomly away from the recognition sites. They are oligomeric proteins formed by three subunits: a specificity subunit, a methylation subunit, and a restriction subunit. We solved the crystal structure of a specificity subunit from Methanococcus jannaschii at 2.4-A resolution. Two highly conserved regions (CRs) in the middle and at the C terminus form a coiled-coil of long antiparallel alpha-helices. Two target recognition domains form globular structures with almost identical topologies and two separate DNA binding clefts with a modeled DNA helix axis positioned across the CR helices. The structure suggests that the coiled-coil CRs act as a molecular ruler for the separation between two recognized DNA sequences. Furthermore, the relative orientation of the two DNA binding clefts suggests kinking of bound dsDNA and exposing of target adenines from the recognized DNA sequences.
Kim
Jeong-Sun
JS
Department of Chemistry, University of California, Berkeley, CA 94720, USA.
DeGiovanni
Andy
A
Jancarik
Jaru
J
Adams
Paul D
PD
Yokota
Hisao
H
Kim
Rosalind
R
Kim
Sung-Hou
SH
D000595:Amino Acid Sequence; D018360:Crystallography, X-Ray; D004262:DNA Restriction Enzymes / Q000737:chemistry / Q000378:metabolism*; D004269:DNA, Bacterial / Q000378:metabolism*; D017017:Methanococcus / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
D004269:DNA, Bacterial; D004262:DNA Restriction Enzymes
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