Arrangement of RecA Protein in Its Active Filament Determined by Polarized-light Spectroscopy

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2002 Aug 24

PMID 12193645

Citations 11

Authors

Katsumi Morimatsu

Masayuki Takahashi

Bengt Norden

Affiliations

Soon will be listed here.

Abstract

Linear dichroism (LD) polarized-light spectroscopy is used to determine the arrangement of RecA in its large filamentous complex with DNA, active in homologous recombination. Angular orientation data for two tryptophan and seven tyrosine residues, deduced from differential LD of wild-type RecA vs. mutants that were engineered to attenuate the UV absorption of selected residues, revealed a rotation by some 40 degrees of the RecA subunits relative to the arrangement in crystal without DNA. In addition, conformational changes are observed for tyrosine residues assigned to be involved in DNA binding and in RecA-RecA contacts, thus potentially related to the global structure of the filament and its biological function. The presented spectroscopic approach, called "Site-Specific Linear Dichroism" (SSLD), may find forceful applications also to other biologically important fibrous complexes not amenable to x-ray crystallographic or NMR structural analysis.

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References

MORIMATSU K, Funakoshi T, Horii T, Takahashi M . Interaction of tyrosine 65 of RecA protein with the first and second DNA strands. J Mol Biol. 2001; 306(2):189-99. DOI: 10.1006/jmbi.2000.4382. View

Wang Y, Adzuma K . Differential proximity probing of two DNA binding sites in the Escherichia coli recA protein using photo-cross-linking methods. Biochemistry. 1996; 35(11):3563-71. DOI: 10.1021/bi952438v. View

Timmins P, Ruigrok R, DiCapua E . The solution structure of recA filaments by small angle neutron scattering. Biochimie. 1991; 73(2-3):227-30. DOI: 10.1016/0300-9084(91)90206-g. View

Norden B, Elvingson C, Jonsson M, AKERMAN B . Microscopic behaviour of DNA during electrophoresis: electrophoretic orientation. Q Rev Biophys. 1991; 24(2):103-64. DOI: 10.1017/s0033583500003395. View

Horii T, Ozawa N, Ogawa T, Ogawa H . Inhibitory effects of N- and C-terminal truncated Escherichia coli recA gene products on functions of the wild-type recA gene. J Mol Biol. 1992; 223(1):105-14. DOI: 10.1016/0022-2836(92)90719-z. View

Story R, Weber I, Steitz T . The structure of the E. coli recA protein monomer and polymer. Nature. 1992; 355(6358):318-25. DOI: 10.1038/355318a0. View

Norden B, Elvingson C, Kubista M, Sjoberg B, Ryberg H, Ryberg M . Structure of RecA-DNA complexes studied by combination of linear dichroism and small-angle neutron scattering measurements on flow-oriented samples. J Mol Biol. 1992; 226(4):1175-91. DOI: 10.1016/0022-2836(92)91060-3. View

Hagmar P, Norden B, Baty D, Chartier M, Takahashi M . Structure of DNA-RecA complexes studied by residue differential linear dichroism and fluorescence spectroscopy for a genetically engineered RecA protein. J Mol Biol. 1992; 226(4):1193-205. DOI: 10.1016/0022-2836(92)91061-s. View

Yu X, Egelman E . Structural data suggest that the active and inactive forms of the RecA filament are not simply interconvertible. J Mol Biol. 1992; 227(1):334-46. DOI: 10.1016/0022-2836(92)90702-l. View

10.

Eriksson S, Norden B, MORIMATSU K, Horii T, Takahashi M . Role of tyrosine residue 264 of RecA for the binding of cofactor and DNA. J Biol Chem. 1993; 268(3):1811-6. View

11.

MORIMATSU K, Horii T, Takahashi M . Interaction of Tyr103 and Tyr264 of the RecA protein with DNA and nucleotide cofactors. Fluorescence study of engineered proteins. Eur J Biochem. 1995; 228(3):779-85. DOI: 10.1111/j.1432-1033.1995.tb20323.x. View

12.

MORIMATSU K, Horii T . Analysis of the DNA binding site of Escherichia coli RecA protein. Adv Biophys. 1995; 31:23-48. DOI: 10.1016/0065-227x(95)99381-x. View

13.

Ellouze C, Takahashi M, Wittung P, Mortensen K, Schnarr M, Norden B . Evidence for elongation of the helical pitch of the RecA filament upon ATP and ADP binding using small-angle neutron scattering. Eur J Biochem. 1995; 233(2):579-83. DOI: 10.1111/j.1432-1033.1995.579_2.x. View

14.

Malkov V, Camerini-Otero R . Photocross-links between single-stranded DNA and Escherichia coli RecA protein map to loops L1 (amino acid residues 157-164) and L2 (amino acid residues 195-209). J Biol Chem. 1995; 270(50):30230-3. DOI: 10.1074/jbc.270.50.30230. View

15.

MORIMATSU K, Horii T . DNA-binding surface of RecA protein photochemical cross-linking of the first DNA binding site on RecA filament. Eur J Biochem. 1995; 234(3):695-705. DOI: 10.1111/j.1432-1033.1995.695_a.x. View

16.

Rehrauer W, Kowalczykowski S . The DNA binding site(s) of the Escherichia coli RecA protein. J Biol Chem. 1996; 271(20):11996-2002. DOI: 10.1074/jbc.271.20.11996. View

17.

MORIMATSU K, Maraboeuf F, Hagmar P, Norden B, Horii T, Takahashi M . Roles of Tyr103 and Tyr264 in the regulation of RecA-DNA interactions by nucleotide cofactors. Eur J Biochem. 1996; 240(1):91-7. DOI: 10.1111/j.1432-1033.1996.0091h.x. View

18.

Roca A, Cox M . RecA protein: structure, function, and role in recombinational DNA repair. Prog Nucleic Acid Res Mol Biol. 1997; 56:129-223. DOI: 10.1016/s0079-6603(08)61005-3. View

19.

Aihara H, Ito Y, Kurumizaka H, Terada T, Yokoyama S, Shibata T . An interaction between a specified surface of the C-terminal domain of RecA protein and double-stranded DNA for homologous pairing. J Mol Biol. 1998; 274(2):213-21. DOI: 10.1006/jmbi.1997.1403. View

20.

Norden B, Wittung-Stafshede P, Ellouze C, Kim H, Mortensen K, Takahashi M . Base orientation of second DNA in RecA.DNA filaments. Analysis by combination of linear dichroism and small angle neutron scattering in flow-oriented solution. J Biol Chem. 1998; 273(25):15682-6. DOI: 10.1074/jbc.273.25.15682. View