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PDBsum entry 3cmu

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protein dna_rna ligands metals links
Recombination/DNA PDB id
3cmu
Jmol
Contents
Protein chain
1937 a.a.
DNA/RNA
Ligands
ALF ×6
ADP ×6
Metals
_MG ×6
PDB id:
3cmu
Name: Recombination/DNA
Title: Mechanism of homologous recombination from the reca- ssdna/dsdna structures
Structure: DNA (5'- d( Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dtp Dt)-3'). Chain: b. Engineered: yes. Protein reca. Chain: a. Synonym: recombinase a. Engineered: yes
Source: Synthetic: yes. Escherichia coli
Resolution:
4.20Å     R-factor:   0.276     R-free:   0.298
Authors: N.P.Pavletich
Key ref:
Z.Chen et al. (2008). Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures. Nature, 453, 489-484. PubMed id: 18497818 DOI: 10.1038/nature06971
Date:
24-Mar-08     Release date:   20-May-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A7G6  (RECA_ECOLI) -  Protein RecA
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
353 a.a.
1937 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 18 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     response to stress   9 terms 
  Biochemical function     nucleotide binding     8 terms  

 

 
DOI no: 10.1038/nature06971 Nature 453:489-484 (2008)
PubMed id: 18497818  
 
 
Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures.
Z.Chen, H.Yang, N.P.Pavletich.
 
  ABSTRACT  
 
The RecA family of ATPases mediates homologous recombination, a reaction essential for maintaining genomic integrity and for generating genetic diversity. RecA, ATP and single-stranded DNA (ssDNA) form a helical filament that binds to double-stranded DNA (dsDNA), searches for homology, and then catalyses the exchange of the complementary strand, producing a new heteroduplex. Here we have solved the crystal structures of the Escherichia coli RecA-ssDNA and RecA-heteroduplex filaments. They show that ssDNA and ATP bind to RecA-RecA interfaces cooperatively, explaining the ATP dependency of DNA binding. The ATP gamma-phosphate is sensed across the RecA-RecA interface by two lysine residues that also stimulate ATP hydrolysis, providing a mechanism for DNA release. The DNA is underwound and stretched globally, but locally it adopts a B-DNA-like conformation that restricts the homology search to Watson-Crick-type base pairing. The complementary strand interacts primarily through base pairing, making heteroduplex formation strictly dependent on complementarity. The underwound, stretched filament conformation probably evolved to destabilize the donor duplex, freeing the complementary strand for homology sampling.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Structure of the presynaptic nucleoprotein filament. a, Structure of the RecA[6]–(ADP-AlF[4]-Mg)[6]–(dT)[18] complex. The six RecA protomers are numbered from the N-terminal RecA of the fusion protein and are coloured pink, brown, green, cyan, purple and magenta, respectively. Only 15 of the 18 nucleotides are ordered (red). The DNA backbone is traced by a red coil. The six ADP-AlF[4]-Mg molecules are coloured gold. The five individual rotation/translation axes that relate adjacent RecA protomers are shown as grey vertical lines. b, The L1 and L2 loop regions and the F and G helices that bind to ssDNA are coloured and numbered as in a, with the rest of each RecA structure omitted for clarity. The ssDNA is numbered starting with the 5'-most nucleotide in each nucleotide triplet. The 5'-most and 3'-most nucleotide triplets have only two and one ordered nucleotides, respectively. Portions of the L1 and L2 loops of the C-terminal RecA are disordered (dashed lines).
Figure 4.
Figure 4: Structure of the postsynaptic nucleoprotein filament. a, Structure of the RecA[5]–(ADP-AlF[4]-Mg)[5]–(dT)[15]–(dA)[12] complex. The five RecA protomers are coloured as the first five protomers of Fig. 1a. The primary (dT)[15] strand (red) has 13 ordered nucleotides, and the complementary (dA)[12] strand (magenta) has 10 ordered nucleotides. b, View of the heteroduplex looking down the filament axis, showing the three central base-pair triplets (of RecA^2, RecA^3 and RecA^4).
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2008, 453, 489-484) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23103864 J.C.Bell, J.L.Plank, C.C.Dombrowski, and S.C.Kowalczykowski (2012).
Direct imaging of RecA nucleation and growth on single molecules of SSB-coated ssDNA.
  Nature, 491, 274-278.  
23103870 S.T.Lovett (2012).
Biochemistry: A glimpse of molecular competition.
  Nature, 491, 198-200.  
20809507 A.G.Cherstvy (2011).
DNA-DNA sequence homology recognition: physical mechanisms and open questions.
  J Mol Recognit, 24, 283-287.  
20386943 C.Carra, and F.A.Cucinotta (2011).
Binding selectivity of RecA to a single stranded DNA, a computational approach.
  J Mol Model, 17, 133-150.  
20817928 D.Ristic, R.Kanaar, and C.Wyman (2011).
Visualizing RAD51-mediated joint molecules: implications for recombination mechanism and the effect of sequence heterology.
  Nucleic Acids Res, 39, 155-167.  
21245047 E.Feinstein, C.Danilowicz, A.Conover, R.Gunaratne, N.Kleckner, and M.Prentiss (2011).
Single-molecule studies of the stringency factors and rates governing the polymerization of RecA on double-stranded DNA.
  Nucleic Acids Res, 39, 3781-3791.  
21964332 K.E.Duderstadt, K.Chuang, and J.M.Berger (2011).
DNA stretching by bacterial initiators promotes replication origin opening.
  Nature, 478, 209-213.
PDB code: 3r8f
  21375680 M.Takaku, T.Kainuma, T.Ishida-Takaku, S.Ishigami, H.Suzuki, S.Tashiro, R.W.van Soest, Y.Nakao, and H.Kurumizaka (2011).
Halenaquinone, a chemical compound that specifically inhibits the secondary DNA binding of RAD51.
  Genes Cells, 16, 427-436.  
21458462 V.E.Galkin, R.L.Britt, L.B.Bane, X.Yu, M.M.Cox, and E.H.Egelman (2011).
Two modes of binding of DinI to RecA filament provide a new insight into the regulation of SOS response by DinI protein.
  J Mol Biol, 408, 815-824.  
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.  
20180912 A.Maréchal, and N.Brisson (2010).
Recombination and the maintenance of plant organelle genome stability.
  New Phytol, 186, 299-317.  
20507912 A.Saladin, C.Amourda, P.Poulain, N.Férey, M.Baaden, M.Zacharias, O.Delalande, and C.Prévost (2010).
Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments.
  Nucleic Acids Res, 38, 6313-6323.  
20877908 B.Feng, K.Frykholm, B.Nordén, and F.Westerlund (2010).
DNA strand exchange catalyzed by molecular crowding in PEG solutions.
  Chem Commun (Camb), 46, 8231-8233.  
20581116 C.Manfredi, Y.Suzuki, T.Yadav, K.Takeyasu, and J.C.Alonso (2010).
RecO-mediated DNA homology search and annealing is facilitated by SsbA.
  Nucleic Acids Res, 38, 6920-6929.  
20379135 E.Crozat, A.Meglio, J.F.Allemand, C.E.Chivers, M.Howarth, C.Vénien-Bryan, I.Grainge, and D.J.Sherratt (2010).
Separating speed and ability to displace roadblocks during DNA translocation by FtsK.
  EMBO J, 29, 1423-1433.  
19875419 E.Rajendra, and A.R.Venkitaraman (2010).
Two modules in the BRC repeats of BRCA2 mediate structural and functional interactions with the RAD51 recombinase.
  Nucleic Acids Res, 38, 82-96.  
20551169 F.Cole, S.Keeney, and M.Jasin (2010).
Evolutionary conservation of meiotic DSB proteins: more than just Spo11.
  Genes Dev, 24, 1201-1207.  
21143322 I.V.Bakhlanova, A.V.Dudkina, D.M.Baitin, K.L.Knight, M.M.Cox, and V.A.Lanzov (2010).
Modulating cellular recombination potential through alterations in RecA structure and regulation.
  Mol Microbiol, 78, 1523-1538.  
20371520 J.Chen, N.Villanueva, M.A.Rould, and S.W.Morrical (2010).
Insights into the mechanism of Rad51 recombinase from the structure and properties of a filament interface mutant.
  Nucleic Acids Res, 38, 4889-4906.
PDB code: 3lda
20953173 J.Lipfert, J.W.Kerssemakers, T.Jager, and N.H.Dekker (2010).
Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments.
  Nat Methods, 7, 977-980.  
  21129202 J.Liu, and S.W.Morrical (2010).
Assembly and dynamics of the bacteriophage T4 homologous recombination machinery.
  Virol J, 7, 357.  
20308162 L.T.Chen, and A.H.Wang (2010).
A rationally designed peptide enhances homologous recombination in vitro and resistance to DNA damaging agents in vivo.
  Nucleic Acids Res, 38, 4361-4371.  
20177395 M.E.Moynahan, and M.Jasin (2010).
Mitotic homologous recombination maintains genomic stability and suppresses tumorigenesis.
  Nat Rev Mol Cell Biol, 11, 196-207.  
20176965 M.P.Hui, V.E.Galkin, X.Yu, A.Z.Stasiak, A.Stasiak, M.K.Waldor, and E.H.Egelman (2010).
ParA2, a Vibrio cholerae chromosome partitioning protein, forms left-handed helical filaments on DNA.
  Proc Natl Acad Sci U S A, 107, 4590-4595.  
19910465 R.L.Britt, N.Haruta, S.L.Lusetti, S.Chitteni-Pattu, R.B.Inman, and M.M.Cox (2010).
Disassembly of Escherichia coli RecA E38K/DeltaC17 nucleoprotein filaments is required to complete DNA strand exchange.
  J Biol Chem, 285, 3211-3226.  
  20981145 R.Morita, S.Nakane, A.Shimada, M.Inoue, H.Iino, T.Wakamatsu, K.Fukui, N.Nakagawa, R.Masui, and S.Kuramitsu (2010).
Molecular mechanisms of the whole DNA repair system: a comparison of bacterial and eukaryotic systems.
  J Nucleic Acids, 2010, 179594.  
20061135 S.Myong, and T.Ha (2010).
Stepwise translocation of nucleic acid motors.
  Curr Opin Struct Biol, 20, 121-127.  
20096651 V.Marini, and L.Krejci (2010).
Srs2: the "Odd-Job Man" in DNA repair.
  DNA Repair (Amst), 9, 268-275.  
20015079 W.Kagawa, and H.Kurumizaka (2010).
From meiosis to postmeiotic events: uncovering the molecular roles of the meiosis-specific recombinase Dmc1.
  FEBS J, 277, 590-598.  
21070965 Y.Savir, and T.Tlusty (2010).
RecA-mediated homology search as a nearly optimal signal detection system.
  Mol Cell, 40, 388-396.  
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.  
19138689 A.M.Makhov, A.Sen, X.Yu, M.N.Simon, J.D.Griffith, and E.H.Egelman (2009).
The bipolar filaments formed by herpes simplex virus type 1 SSB/recombination protein (ICP8) suggest a mechanism for DNA annealing.
  J Mol Biol, 386, 273-279.  
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.  
19666582 C.Danilowicz, C.Limouse, K.Hatch, A.Conover, V.W.Coljee, N.Kleckner, and M.Prentiss (2009).
The structure of DNA overstretched from the 5'5' ends differs from the structure of DNA overstretched from the 3'3' ends.
  Proc Natl Acad Sci U S A, 106, 13196-13201.  
19514040 C.Guo, G.Li, Z.Liu, L.Sun, Y.Sun, F.Xu, Y.Zhang, T.Yang, and Z.Li (2009).
Influence of polyelectrolyte on DNA-RecA nucleoprotein filaments: poly-L-lysine used as a model.
  Chemphyschem, 10, 1624-1629.  
19492398 C.Prévost, M.Takahashi, and R.Lavery (2009).
Deforming DNA: from physics to biology.
  Chemphyschem, 10, 1399-1404.  
19540850 D.Lucarelli, Y.A.Wang, V.E.Galkin, X.Yu, D.B.Wigley, and E.H.Egelman (2009).
The RecB nuclease domain binds to RecA-DNA filaments: implications for filament loading.
  J Mol Biol, 391, 269-274.  
19884492 H.Arata, A.Dupont, J.Miné-Hattab, L.Disseau, A.Renodon-Cornière, M.Takahashi, J.L.Viovy, and G.Cappello (2009).
Direct observation of twisting steps during Rad51 polymerization on DNA.
  Proc Natl Acad Sci U S A, 106, 19239-19244.  
19383795 H.Liu, Y.Shi, X.S.Chen, and A.Warshel (2009).
Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases.
  Proc Natl Acad Sci U S A, 106, 7449-7454.  
19555451 J.E.Long, N.Renzette, and S.J.Sandler (2009).
Suppression of constitutive SOS expression by recA4162 (I298V) and recA4164 (L126V) requires UvrD and RecX in Escherichia coli K-12.
  Mol Microbiol, 73, 226-239.  
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.  
19060884 J.van Mameren, M.Modesti, R.Kanaar, C.Wyman, E.J.Peterman, and G.J.Wuite (2009).
Counting RAD51 proteins disassembling from nucleoprotein filaments under tension.
  Nature, 457, 745-748.  
19470566 K.M.Sinha, M.C.Unciuleac, M.S.Glickman, and S.Shuman (2009).
AdnAB: a new DSB-resecting motor-nuclease from mycobacteria.
  Genes Dev, 23, 1423-1437.  
19666566 M.M.Cox (2009).
A new look at the human Rad51 protein.
  Proc Natl Acad Sci U S A, 106, 13147-13148.  
19605345 P.Singh, P.Tripathi, G.H.Silva, A.Pingoud, and K.Muniyappa (2009).
Characterization of Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease, reveals a unique mode of DNA binding, helical distortion, and cleavage compared with a canonical LAGLIDADG homing endonuclease.
  J Biol Chem, 284, 25912-25928.  
19327367 R.B.Robertson, D.N.Moses, Y.Kwon, P.Chan, W.Zhao, P.Chi, H.Klein, P.Sung, and E.C.Greene (2009).
Visualizing the disassembly of S. cerevisiae Rad51 nucleoprotein filaments.
  J Mol Biol, 388, 703-720.  
19625494 R.Lavery, M.Moakher, J.H.Maddocks, D.Petkeviciute, and K.Zakrzewska (2009).
Conformational analysis of nucleic acids revisited: Curves+.
  Nucleic Acids Res, 37, 5917-5929.  
19820696 R.Roy, A.G.Kozlov, T.M.Lohman, and T.Ha (2009).
SSB protein diffusion on single-stranded DNA stimulates RecA filament formation.
  Nature, 461, 1092-1097.  
19729448 T.Masuda, Y.Ito, T.Terada, T.Shibata, and T.Mikawa (2009).
A non-canonical DNA structure enables homologous recombination in various genetic systems.
  J Biol Chem, 284, 30230-30239.
PDB codes: 2rpd 2rpe 2rpf 2rph
19013467 V.E.Galkin, X.Yu, J.Bielnicki, D.Ndjonka, C.E.Bell, and E.H.Egelman (2009).
Cleavage of bacteriophage lambda cI repressor involves the RecA C-terminal domain.
  J Mol Biol, 385, 779-787.  
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.  
19465774 Y.Li, Y.He, and Y.Luo (2009).
Conservation of a conformational switch in RadA recombinase from Methanococcus maripaludis.
  Acta Crystallogr D Biol Crystallogr, 65, 602-610.
PDB codes: 3etl 3ew9 3ewa
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
19102758 A.I.Roca, A.E.Almada, and A.C.Abajian (2008).
ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family.
  BMC Bioinformatics, 9, 554.  
19436497 E.H.Egelman (2008).
Problems in fitting high resolution structures into electron microscopic reconstructions.
  HFSP J, 2, 324-331.  
18953036 G.Lahoud, K.Arar, Y.M.Hou, and H.Gamper (2008).
RecA-mediated strand invasion of DNA by oligonucleotides substituted with 2-aminoadenine and 2-thiothymine.
  Nucleic Acids Res, 36, 6806-6815.  
18583359 I.Sakane, C.Kamataki, Y.Takizawa, M.Nakashima, S.Toki, H.Ichikawa, S.Ikawa, T.Shibata, and H.Kurumizaka (2008).
Filament formation and robust strand exchange activities of the rice DMC1A and DMC1B proteins.
  Nucleic Acids Res, 36, 4266-4276.  
19116657 J.E.Long, N.Renzette, R.C.Centore, and S.J.Sandler (2008).
Differential requirements of two recA mutants for constitutive SOS expression in Escherichia coli K-12.
  PLoS ONE, 3, e4100.  
18603529 J.M.Cox, H.Li, E.A.Wood, S.Chitteni-Pattu, R.B.Inman, and M.M.Cox (2008).
Defective Dissociation of a "Slow" RecA Mutant Protein Imparts an Escherichia coli Growth Defect.
  J Biol Chem, 283, 24909-24921.  
19020353 J.R.Prabu, G.P.Manjunath, N.R.Chandra, K.Muniyappa, and M.Vijayan (2008).
Functionally important movements in RecA molecules and filaments: studies involving mutation and environmental changes.
  Acta Crystallogr D Biol Crystallogr, 64, 1146-1157.
PDB codes: 2zr0 2zr7 2zr9 2zra 2zrb 2zrc 2zrd 2zre 2zrf 2zrg 2zrh 2zri 2zrj 2zrk 2zrl 2zrm 2zrn 2zro 2zrp
18927106 P.S.Malik, and L.S.Symington (2008).
Rad51 gain-of-function mutants that exhibit high affinity DNA binding cause DNA damage sensitivity in the absence of Srs2.
  Nucleic Acids Res, 36, 6504-6510.  
18497811 S.C.Kowalczykowski (2008).
Structural biology: snapshots of DNA repair.
  Nature, 453, 463-466.  
18650935 S.Ragone, J.D.Maman, N.Furnham, and L.Pellegrini (2008).
Structural basis for inhibition of homologous recombination by the RecX protein.
  EMBO J, 27, 2259-2269.
PDB code: 3c1d
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 code is shown on the right.