PDBsum entry 1b22

DNA binding protein

PDB id

1b22

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Contents

			Protein chain

					70 a.a. *

* Residue conservation analysis

PDB id:

1b22

Links
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Name:

DNA binding protein

Title:

Rad51 (n-terminal domain)

Structure:

DNA repair protein rad51. Chain: a. Fragment: n-terminal domain. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

30 models

Authors:

H.Aihara,Y.Ito,H.Kurumizaka,S.Yokoyama,T.Shibata,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

H.Aihara et al. (1999). The N-terminal domain of the human Rad51 protein binds DNA: structure and a DNA binding surface as revealed by NMR. J Mol Biol, 290, 495-504. PubMed id: 10390347 DOI: 10.1006/jmbi.1999.2904

Date:

04-Dec-98

Release date:

03-Dec-99

PROCHECK

	Headers

	References

Protein chain

Q06609 (RAD51_HUMAN) - DNA repair protein RAD51 homolog 1 from Homo sapiens

Seq: Struc:					339 a.a. 70 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

DOI no: 10.1006/jmbi.1999.2904	J Mol Biol 290:495-504 (1999)
PubMed id: 10390347

The N-terminal domain of the human Rad51 protein binds DNA: structure and a DNA binding surface as revealed by NMR.
H.Aihara, Y.Ito, H.Kurumizaka, S.Yokoyama, T.Shibata.

ABSTRACT

Human Rad51 protein (HsRad51) is a homolog of Escherichia coli RecA protein, and functions in DNA repair and recombination. In higher eukaryotes, Rad51 protein is essential for cell viability. The N-terminal region of HsRad51 is highly conserved among eukaryotic Rad51 proteins but is absent from RecA, suggesting a Rad51-specific function for this region. Here, we have determined the structure of the N-terminal part of HsRad51 by NMR spectroscopy. The N-terminal region forms a compact domain consisting of five short helices, which shares structural similarity with a domain of endonuclease III, a DNA repair enzyme of E. coli. NMR experiments did not support the involvement of the N-terminal domain in HsRad51-HsBrca2 interaction or the self-association of HsRad51 as proposed by previous studies. However, NMR tiration experiments demonstrated a physical interaction of the domain with DNA, and allowed mapping of the DNA binding surface. Mutation analysis showed that the DNA binding surface is essential for double-stranded and single-stranded DNA binding of HsRad51. Our results suggest the presence of a DNA binding site on the outside surface of the HsRad51 filament and provide a possible explanation for the regulation of DNA binding by phosphorylation within the N-terminal domain.

Selected figure(s)



	Figure 4. Figure 4. Chemical shift pertur- bation upon the DNA binding. (a) Expansions of 1 H- 15 N HSQC spectra of 15 N-labeled HsRad51(1-114) in the absence (black contours) and presence (red contours) of a three molar equivalent of 12 bp double- stranded DNA. The crosspeaks that shift upon the addition of DNA are indicated. (b), (c) Chemical shift change of backbone 1 H and 15 N calculated as [(deltad 1 H) 2 + (deltad 15 N) 2 ] 1/2		Figure 6. Figure 6. Structural similarity of the N-terminal domain of HsRad51 and the six-helix barrel domain of E. coli endonuclease III. Stereodiagram showing the backbone superposition of HsRad51 (red, residues 26- 84) and endonuclease III (cyan, residues 31-99) (Thayer et al., 1995). The r.m.s.d. along the C a atoms of residues 26-29, 32-35, 41-45, 46-49, 50-53, 55-65 and 67-84 of HsRad51 with the corresponding part of endonuclease III is 2.86 Å . The Figure was generated using the program MIDASPlus (Ferrin et al., 1988).

Figures were selected by the author.

Author's comment

It is shown that the N-terminal part of the human Rad51 protein constitutes a DNA binding domain. The domain may lie on the outside surface of the Rad51 filament, and this suggests the critical role of this domain in the homologous pairing reaction.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20062530

A.L.Okorokov, Y.L.Chaban, D.V.Bugreev, J.Hodgkinson, A.V.Mazin, and E.V.Orlova (2010).
Structure of the hDmc1-ssDNA filament reveals the principles of its architecture.

PLoS One, 5, e8586.

20403813

Y.Takizawa, Y.Qing, M.Takaku, T.Ishida, Y.Morozumi, T.Tsujita, T.Kogame, K.Hirota, M.Takahashi, T.Shibata, H.Kurumizaka, and S.Takeda (2010).
GEMIN2 promotes accumulation of RAD51 at double-strand breaks in homologous recombination.

Nucleic Acids Res, 38, 5059-5074.

19066203

A.A.Grigorescu, J.H.Vissers, D.Ristic, Y.Z.Pigli, T.W.Lynch, C.Wyman, and P.A.Rice (2009).
Inter-subunit interactions that coordinate Rad51's activities.

Nucleic Acids Res, 37, 557-567.

19587234

A.Reymer, K.Frykholm, K.Morimatsu, M.Takahashi, and B.Nordén (2009).
Structure of human Rad51 protein filament from molecular modeling and site-specific linear dichroism spectroscopy.

Proc Natl Acad Sci U S A, 106, 13248-13253.

19338667

C.D.Lee, and T.F.Wang (2009).
The N-terminal domain of Escherichia coli RecA have multiple functions in promoting homologous recombination.

J Biomed Sci, 16, 37.

19076215

J.Hikiba, Y.Takizawa, S.Ikawa, T.Shibata, and H.Kurumizaka (2009).
Biochemical analysis of the human DMC1-I37N polymorphism.

FEBS J, 276, 457-465.

19336413

T.Ishida, Y.Takizawa, T.Kainuma, J.Inoue, T.Mikawa, T.Shibata, H.Suzuki, S.Tashiro, and H.Kurumizaka (2009).
DIDS, a chemical compound that inhibits RAD51-mediated homologous pairing and strand exchange.

Nucleic Acids Res, 37, 3367-3376.

19033358

X.P.Zhang, V.E.Galkin, X.Yu, E.H.Egelman, and W.D.Heyer (2009).
Loop 2 in Saccharomyces cerevisiae Rad51 protein regulates filament formation and ATPase activity.

Nucleic Acids Res, 37, 158-171.

19447914

Y.Morozumi, Y.Takizawa, M.Takaku, and H.Kurumizaka (2009).
Human PSF binds to RAD51 and modulates its homologous-pairing and strand-exchange activities.

Nucleic Acids Res, 37, 4296-4307.

19295907

Y.W.Chang, T.P.Ko, C.D.Lee, Y.C.Chang, K.A.Lin, C.S.Chang, A.H.Wang, and T.F.Wang (2009).
Three new structures of left-handed RADA helical filaments: structural flexibility of N-terminal domain is critical for recombinase activity.

PLoS ONE, 4, e4890.

PDB codes:

2zub 2zuc 2zud

18566005

J.Hikiba, K.Hirota, W.Kagawa, S.Ikawa, T.Kinebuchi, I.Sakane, Y.Takizawa, S.Yokoyama, B.Mandon-Pépin, A.Nicolas, T.Shibata, K.Ohta, and H.Kurumizaka (2008).
Structural and functional analyses of the DMC1-M200V polymorphism found in the human population.

Nucleic Acids Res, 36, 4181-4190.

PDB code:

2zjb

18940471

J.T.Holt, W.P.Toole, V.R.Patel, H.Hwang, and E.T.Brown (2008).
Restoration of CAPAN-1 cells with functional BRCA2 provides insight into the DNA repair activity of individuals who are heterozygous for BRCA2 mutations.

Cancer Genet Cytogenet, 186, 85-94.

18535008

S.D.Sheridan, X.Yu, R.Roth, J.E.Heuser, M.G.Sehorn, P.Sung, E.H.Egelman, and D.K.Bishop (2008).
A comparative analysis of Dmc1 and Rad51 nucleoprotein filaments.

Nucleic Acids Res, 36, 4057-4066.

17329376

L.T.Chen, T.P.Ko, Y.C.Chang, K.A.Lin, C.S.Chang, A.H.Wang, and T.F.Wang (2007).
Crystal structure of the left-handed archaeal RadA helical filament: identification of a functional motif for controlling quaternary structures and enzymatic functions of RecA family proteins.

Nucleic Acids Res, 35, 1787-1801.

PDB code:

2dfl

17848989

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

PLoS ONE, 2, e858.

PDB code:

2z43

16765891

V.E.Galkin, Y.Wu, X.P.Zhang, X.Qian, Y.He, X.Yu, W.D.Heyer, Y.Luo, and E.H.Egelman (2006).
The Rad51/RadA N-terminal domain activates nucleoprotein filament ATPase activity.

Structure, 14, 983-992.

PDB code:

2gdj

16798872

Z.Lin, H.Kong, M.Nei, and H.Ma (2006).
Origins and evolution of the recA/RAD51 gene family: evidence for ancient gene duplication and endosymbiotic gene transfer.

Proc Natl Acad Sci U S A, 103, 10328-10333.

15755748

A.Ariza, D.J.Richard, M.F.White, and C.S.Bond (2005).
Conformational flexibility revealed by the crystal structure of a crenarchaeal RadA.

Nucleic Acids Res, 33, 1465-1473.

PDB code:

2bke

16194225

C.E.Bell (2005).
Structure and mechanism of Escherichia coli RecA ATPase.

Mol Microbiol, 58, 358-366.

15937124

V.E.Galkin, F.Esashi, X.Yu, S.Yang, S.C.West, and E.H.Egelman (2005).
BRCA2 BRC motifs bind RAD51-DNA filaments.

Proc Natl Acad Sci U S A, 102, 8537-8542.

15908697

X.P.Zhang, K.I.Lee, J.A.Solinger, K.Kiianitsa, and W.D.Heyer (2005).
Gly-103 in the N-terminal domain of Saccharomyces cerevisiae Rad51 protein is critical for DNA binding.

J Biol Chem, 280, 26303-26311.

15537659

Y.Wu, X.Qian, Y.He, I.A.Moya, and Y.Luo (2005).
Crystal structure of an ATPase-active form of Rad51 homolog from Methanococcus voltae. Insights into potassium dependence.

J Biol Chem, 280, 722-728.

PDB code:

1xu4

15235592

A.B.Conway, T.W.Lynch, Y.Zhang, G.S.Fortin, C.W.Fung, L.S.Symington, and P.A.Rice (2004).
Crystal structure of a Rad51 filament.

Nat Struct Mol Biol, 11, 791-796.

PDB code:

1szp

15568977

B.O.Krogh, and L.S.Symington (2004).
Recombination proteins in yeast.

Annu Rev Genet, 38, 233-271.

14704354

K.A.Miller, D.Sawicka, D.Barsky, and J.S.Albala (2004).
Domain mapping of the Rad51 paralog protein complexes.

Nucleic Acids Res, 32, 169-178.

15056657

M.E.Stauffer, and W.J.Chazin (2004).
Physical interaction between replication protein A and Rad51 promotes exchange on single-stranded DNA.

J Biol Chem, 279, 25638-25645.

15598351

S.Cheek, Y.Qi, S.S.Krishna, L.N.Kinch, and N.V.Grishin (2004).
4SCOPmap: automated assignment of protein structures to evolutionary superfamilies.

BMC Bioinformatics, 5, 197.

15590830

V.I.Shalguev, Y.V.Kil, L.V.Yurchenko, E.A.Namsaraev, and V.A.Lanzov (2004).
Rad51 protein from the thermotolerant yeast Pichia angusta as a typical but thermodependent member of the Rad51 family.

Eukaryot Cell, 3, 1567-1573.

12941707

D.S.Shin, L.Pellegrini, D.S.Daniels, B.Yelent, L.Craig, D.Bates, D.S.Yu, M.K.Shivji, C.Hitomi, A.S.Arvai, N.Volkmann, H.Tsuruta, T.L.Blundell, A.R.Venkitaraman, and J.A.Tainer (2003).
Full-length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2.

EMBO J, 22, 4566-4576.

PDB code:

1pzn

12427746

Y.C.Lio, A.V.Mazin, S.C.Kowalczykowski, D.J.Chen, and D.J.Chen (2003).
Complex formation by the human Rad51B and Rad51C DNA repair proteins and their activities in vitro.

J Biol Chem, 278, 2469-2478.

12065428

G.S.Fortin, and L.S.Symington (2002).
Mutations in yeast Rad51 that partially bypass the requirement for Rad55 and Rad57 in DNA repair by increasing the stability of Rad51-DNA complexes.

EMBO J, 21, 3160-3170.

11839741

G.Tombline, C.D.Heinen, K.S.Shim, and R.Fishel (2002).
Biochemical characterization of the human RAD51 protein. III. Modulation of DNA binding by adenosine nucleotides.

J Biol Chem, 277, 14434-14442.

11839739

G.Tombline, and R.Fishel (2002).
Biochemical characterization of the human RAD51 protein. I. ATP hydrolysis.

J Biol Chem, 277, 14417-14425.

12456786

L.S.Symington (2002).
Role of RAD52 epistasis group genes in homologous recombination and double-strand break repair.

Microbiol Mol Biol Rev, 66, 630.

12050150

W.J.Kim, E.J.Park, H.Lee, R.H.Seong, and S.D.Park (2002).
Physical interaction between recombinational proteins Rhp51 and Rad22 in Schizosaccharomyces pombe.

J Biol Chem, 277, 30264-30270.

11170890

D.Thompson, and D.Easton (2001).
Variation in cancer risks, by mutation position, in BRCA2 mutation carriers.

Am J Hum Genet, 68, 410-419.

11331762

H.Kurumizaka, S.Ikawa, M.Nakada, K.Eda, W.Kagawa, M.Takata, S.Takeda, S.Yokoyama, and T.Shibata (2001).
Homologous-pairing activity of the human DNA-repair proteins Xrcc3.Rad51C.

Proc Natl Acad Sci U S A, 98, 5538-5543.

11154282

L.Krejci, J.Damborsky, B.Thomsen, M.Duno, and C.Bendixen (2001).
Molecular dissection of interactions between Rad51 and members of the recombination-repair group.

Mol Cell Biol, 21, 966-976.

11459985

T.Shibata, T.Nishinaka, T.Mikawa, H.Aihara, H.Kurumizaka, S.Yokoyama, and Y.Ito (2001).
Homologous genetic recombination as an intrinsic dynamic property of a DNA structure induced by RecA/Rad51-family proteins: a possible advantage of DNA over RNA as genomic material.

Proc Natl Acad Sci U S A, 98, 8425-8432.

11459984

X.Yu, S.A.Jacobs, S.C.West, T.Ogawa, and E.H.Egelman (2001).
Domain structure and dynamics in the helical filaments formed by RecA and Rad51 on DNA.

Proc Natl Acad Sci U S A, 98, 8419-8424.

11560889

Y.Tsutsui, F.K.Khasanov, H.Shinagawa, H.Iwasaki, and V.I.Bashkirov (2001).
Multiple interactions among the components of the recombinational DNA repair system in Schizosaccharomyces pombe.

Genetics, 159, 91.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.