title: Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications.
abstract: 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.
authors.affiliation: Department of Chemistry, University of California, Berkeley, CA 94720, USA.
authors.forename: Jeong-Sun
authors.initials: JS
authors.lastname: Kim
authors.forename: Andy
authors.initials: A
authors.lastname: DeGiovanni
authors.forename: Jaru
authors.initials: J
authors.lastname: Jancarik
authors.forename: Paul D
authors.initials: PD
authors.lastname: Adams
authors.forename: Hisao
authors.initials: H
authors.lastname: Yokota
authors.forename: Rosalind
authors.initials: R
authors.lastname: Kim
authors.forename: Sung-Hou
authors.initials: SH
authors.lastname: Kim
mesh_terms: 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
chemical_list: D004269:DNA, Bacterial; D004262:DNA Restriction Enzymes
references.citation: Acta Crystallogr D Biol Crystallogr. 1999 Apr;55(Pt 4):849-61
references.pmid: 10089316
references.citation: Science. 1999 Jun 4;284(5420):1667-70
references.pmid: 10356396
references.citation: Nature. 1999 Aug 19;400(6746):787-92
references.pmid: 10466731
references.citation: Cell. 2000 Nov 10;103(4):621-32
references.pmid: 11106732
references.citation: Nat Struct Biol. 2001 Feb;8(2):121-5
references.pmid: 11175899
references.citation: Nature. 2002 Aug 1;418(6897):562-6
references.pmid: 12152085
references.citation: J Mol Biol. 2004 Jan 16;335(3):787-97
references.pmid: 14687574
references.citation: Nucleic Acids Res. 2004 Oct 08;32(18):e138
references.pmid: 15475385
references.citation: EMBO J. 1992 Jan;11(1):233-40
references.pmid: 1740108
references.citation: EMBO J. 1991 Apr;10(4):951-7
references.pmid: 1849078
references.citation: Acta Crystallogr A. 1991 Mar 1;47 ( Pt 2):110-9
references.pmid: 2025413
references.citation: Nucleic Acids Res. 1990 Oct 25;18(20):6069-74
references.pmid: 2235490
references.citation: J Mol Biol. 1989 Oct 5;209(3):335-44
references.pmid: 2585490
references.citation: Methods Enzymol. 1997;276:307-26
references.pmid: 27754618
references.citation: J Mol Biol. 1989 Jan 5;205(1):115-25
references.pmid: 2784505
references.citation: Proc Natl Acad Sci U S A. 1988 Jul;85(13):4677-81
references.pmid: 2838843
references.citation: J Biol Chem. 1985 May 10;260(9):5729-38
references.pmid: 2985610
references.citation: Annu Rev Biochem. 1981;50:285-319
references.pmid: 6267988
references.citation: J Mol Biol. 1983 May 5;166(1):1-19
references.pmid: 6304321
references.citation: Genetics. 1995 Aug;140(4):1187-97
references.pmid: 7498762
references.citation: J Mol Biol. 1994 Oct 14;243(1):1-5
references.pmid: 7932730
references.citation: J Mol Biol. 1994 Aug 5;241(1):35-43
references.pmid: 8051705
references.citation: Microbiol Rev. 1993 Jun;57(2):434-50
references.pmid: 8336674
references.citation: J Mol Biol. 1993 Sep 5;233(1):123-38
references.pmid: 8377180
references.citation: J Mol Biol. 1996 Apr 12;257(4):790-803
references.pmid: 8636982
references.citation: EMBO J. 1996 Nov 15;15(22):6335-47
references.pmid: 8947056
references.citation: J Mol Biol. 1996 Dec 13;264(4):722-33
references.pmid: 8980681
references.citation: Biol Chem. 1998 Apr-May;379(4-5):585-9
references.pmid: 9628361
references.citation: Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21
references.pmid: 9757107
references.citation: EMBO J. 1998 Dec 1;17(23):7118-27
references.pmid: 9843515