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PDBsum entry 1v5w

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protein Protein-protein interface(s) links
Recombination PDB id
1v5w
Jmol
Contents
Protein chain
239 a.a. *
Waters ×17
* Residue conservation analysis
PDB id:
1v5w
Name: Recombination
Title: Crystal structure of the human dmc1 protein
Structure: Meiotic recombination protein dmc1/lim15 homolog. Chain: a, b. Synonym: dmc1. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: dmc1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: 60mer (from PDB file)
Resolution:
3.20Å     R-factor:   0.294     R-free:   0.346
Authors: T.Kinebuchi,W.Kagawa,R.Enomoto,S.Ikawa,T.Shibata,H.Kurumizak S.Yokoyama,Riken Structural Genomics/proteomics Initiative
Key ref:
T.Kinebuchi et al. (2004). Structural basis for octameric ring formation and DNA interaction of the human homologous-pairing protein Dmc1. Mol Cell, 14, 363-374. PubMed id: 15125839 DOI: 10.1016/S1097-2765(04)00218-7
Date:
26-Nov-03     Release date:   18-May-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q14565  (DMC1_HUMAN) -  Meiotic recombination protein DMC1/LIM15 homolog
Seq:
Struc:
340 a.a.
239 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   4 terms 
  Biological process     cell cycle   13 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
DOI no: 10.1016/S1097-2765(04)00218-7 Mol Cell 14:363-374 (2004)
PubMed id: 15125839  
 
 
Structural basis for octameric ring formation and DNA interaction of the human homologous-pairing protein Dmc1.
T.Kinebuchi, W.Kagawa, R.Enomoto, K.Tanaka, K.Miyagawa, T.Shibata, H.Kurumizaka, S.Yokoyama.
 
  ABSTRACT  
 
The human Dmc1 protein, a RecA/Rad51 homolog, is a meiosis-specific DNA recombinase that catalyzes homologous pairing. RecA and Rad51 form helical filaments, while Dmc1 forms an octameric ring. In the present study, we crystallized the full-length human Dmc1 protein and solved the structure of the Dmc1 octameric ring. The monomeric structure of the Dmc1 protein closely resembled those of the human and archaeal Rad51 proteins. In addition to the polymerization motif that was previously identified in the Rad51 proteins, we found another hydrogen bonding interaction at the polymer interface, which could explain why Dmc1 forms stable octameric rings instead of helical filaments. Mutagenesis studies identified the inner and outer basic patches that are important for homologous pairing. The inner patch binds both single-stranded and double-stranded DNAs, while the outer one binds single-stranded DNA. Based on these results, we propose a model for the interaction of the Dmc1 rings with DNA.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. The DNA Binding Sites of Dmc1(A) The dsDNA passes through the central channel of Dmc1. The same side chains as in Figure 3C are shown. (B) Double ring formation by Dmc1. (C) Electrostatic surface potential of the Dmc1 double ring structure, viewed from the side. Positively charged cavities are boxed in (B) and (C), and contain an amino acid residue (R311) essential for ssDNA binding.
Figure 6.
Figure 6. A Model of a Homologous Pairing Intermediate Complex between Dmc1, ssDNA, and dsDNA(A) Schematic representation of dsDNA passing through the central channel of Dmc1. The N-terminal domain (colored yellow) may initially bind to dsDNA, creating a bending stress that could cause the dissociation of the ATPase domain (colored pink).(B) Ternary complex formation by the Dmc1 double ring, ssDNA, and dsDNA requires ATP. The search and the pairing of two homologous sequences could take place at the center of the Dmc1 double ring. The dsDNA is shown entering from one end of the stacked ring. The ssDNA is shown passing through the cavity created by the stacking of two Dmc1 rings.
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2004, 14, 363-374) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20404438 A.Janner (2010).
Form, symmetry and packing of biomacromolecules. I. Concepts and tutorial examples.
  Acta Crystallogr A, 66, 301-311.  
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.  
20236180 N.Horikoshi, Y.Morozumi, M.Takaku, Y.Takizawa, and H.Kurumizaka (2010).
Holliday junction-binding activity of human SPF45.
  Genes Cells, 15, 373-383.  
  20798837 R.K.Chittela, and J.K.Sainis (2010).
Plant DNA recombinases: a long way to go.
  J Nucleic Acids, 2010, 0.  
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.  
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.  
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.  
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.  
19329439 M.Takaku, S.Machida, N.Hosoya, S.Nakayama, Y.Takizawa, I.Sakane, T.Shibata, K.Miyagawa, and H.Kurumizaka (2009).
Recombination Activator Function of the Novel RAD51- and RAD51B-binding Protein, Human EVL.
  J Biol Chem, 284, 14326-14336.  
19622740 R.B.Robertson, D.N.Moses, Y.Kwon, P.Chan, P.Chi, H.Klein, P.Sung, and E.C.Greene (2009).
Structural transitions within human Rad51 nucleoprotein filaments.
  Proc Natl Acad Sci U S A, 106, 12688-12693.  
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.  
19811618 R.Dirks, K.van Dun, C.B.de Snoo, M.van den Berg, C.L.Lelivelt, W.Voermans, L.Woudenberg, J.P.de Wit, K.Reinink, J.W.Schut, E.van der Zeeuw, A.Vogelaar, G.Freymark, E.W.Gutteling, M.N.Keppel, P.van Drongelen, M.Kieny, P.Ellul, A.Touraev, H.Ma, H.de Jong, and E.Wijnker (2009).
Reverse breeding: a novel breeding approach based on engineered meiosis.
  Plant Biotechnol J, 7, 837-845.  
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
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.  
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
18429819 J.Nomme, Y.Takizawa, S.F.Martinez, A.Renodon-Cornière, F.Fleury, P.Weigel, K.Yamamoto, H.Kurumizaka, and M.Takahashi (2008).
Inhibition of filament formation of human Rad51 protein by a small peptide derived from the BRC-motif of the BRCA2 protein.
  Genes Cells, 13, 471-481.  
18402694 M.López-Casamichana, E.Orozco, L.A.Marchat, and C.López-Camarillo (2008).
Transcriptional profile of the homologous recombination machinery and characterization of the EhRAD51 recombinase in response to DNA damage in Entamoeba histolytica.
  BMC Mol Biol, 9, 35.  
18718930 N.Sarai, W.Kagawa, N.Fujikawa, K.Saito, J.Hikiba, K.Tanaka, K.Miyagawa, H.Kurumizaka, and S.Yokoyama (2008).
Biochemical analysis of the N-terminal domain of human RAD54B.
  Nucleic Acids Res, 36, 5441-5450.  
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.  
17515904 F.Esashi, V.E.Galkin, X.Yu, E.H.Egelman, and S.C.West (2007).
Stabilization of RAD51 nucleoprotein filaments by the C-terminal region of BRCA2.
  Nat Struct Mol Biol, 14, 468-474.  
17584917 L.Knizewski, L.N.Kinch, N.V.Grishin, L.Rychlewski, and K.Ginalski (2007).
Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches.
  BMC Struct Biol, 7, 40.  
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
17515903 O.R.Davies, and L.Pellegrini (2007).
Interaction with the BRCA2 C terminus protects RAD51-DNA filaments from disassembly by BRC repeats.
  Nat Struct Mol Biol, 14, 475-483.  
17541404 T.Thorslund, F.Esashi, and S.C.West (2007).
Interactions between human BRCA2 protein and the meiosis-specific recombinase DMC1.
  EMBO J, 26, 2915-2922.  
18066084 T.Thorslund, and S.C.West (2007).
BRCA2: a universal recombinase regulator.
  Oncogene, 26, 7720-7730.  
16432240 A.Granéli, C.C.Yeykal, R.B.Robertson, and E.C.Greene (2006).
Long-distance lateral diffusion of human Rad51 on double-stranded DNA.
  Proc Natl Acad Sci U S A, 103, 1221-1226.  
16689935 C.Rajanikant, M.Kumbhakar, H.Pal, B.J.Rao, and J.K.Sainis (2006).
DNA strand exchange activity of rice recombinase OsDmc1 monitored by fluorescence resonance energy transfer and the role of ATP hydrolysis.
  FEBS J, 273, 1497-1506.  
16838012 M.J.Neale, and S.Keeney (2006).
Clarifying the mechanics of DNA strand exchange in meiotic recombination.
  Nature, 442, 153-158.  
16945962 N.Sarai, W.Kagawa, T.Kinebuchi, A.Kagawa, K.Tanaka, K.Miyagawa, S.Ikawa, T.Shibata, H.Kurumizaka, and S.Yokoyama (2006).
Stimulation of Dmc1-mediated DNA strand exchange by the human Rad54B protein.
  Nucleic Acids Res, 34, 4429-4437.  
16407260 R.Enomoto, T.Kinebuchi, M.Sato, H.Yagi, H.Kurumizaka, and S.Yokoyama (2006).
Stimulation of DNA strand exchange by the human TBPIP/Hop2-Mnd1 complex.
  J Biol Chem, 281, 5575-5581.  
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
16367760 V.M.Navadgi, A.Shukla, R.K.Vempati, and B.J.Rao (2006).
DNA mediated disassembly of hRad51 and hRad52 proteins and recruitment of hRad51 to ssDNA by hRad52.
  FEBS J, 273, 199-207.  
16780572 Y.Matsuo, I.Sakane, Y.Takizawa, M.Takahashi, and H.Kurumizaka (2006).
Roles of the human Rad51 L1 and L2 loops in DNA binding.
  FEBS J, 273, 3148-3159.  
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.  
15897179 C.E.Huang, M.Milutinovich, and D.Koshland (2005).
Rings, bracelet or snaps: fashionable alternatives for Smc complexes.
  Philos Trans R Soc Lond B Biol Sci, 360, 537-542.  
15821864 C.R.Kant, B.J.Rao, and J.K.Sainis (2005).
DNA binding and pairing activity of OsDmc1, a recombinase from rice.
  Plant Mol Biol, 57, 1.  
15917244 D.V.Bugreev, E.I.Golub, A.Z.Stasiak, A.Stasiak, and A.V.Mazin (2005).
Activation of human meiosis-specific recombinase Dmc1 by Ca2+.
  J Biol Chem, 280, 26886-26895.  
16204247 M.H.Lee, Y.C.Chang, E.L.Hong, J.Grubb, C.S.Chang, D.K.Bishop, and T.F.Wang (2005).
Calcium ion promotes yeast Dmc1 activity via formation of long and fine helical filaments with single-stranded DNA.
  J Biol Chem, 280, 40980-40984.  
15899844 S.Sauvageau, A.Z.Stasiak, I.Banville, M.Ploquin, A.Stasiak, and J.Y.Masson (2005).
Fission yeast rad51 and dmc1, two efficient DNA recombinases forming helical nucleoprotein filaments.
  Mol Cell Biol, 25, 4377-4387.  
15956102 T.Akiba, N.Ishii, N.Rashid, M.Morikawa, T.Imanaka, and K.Harata (2005).
Structure of RadB recombinase from a hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1: an implication for the formation of a near-7-fold helical assembly.
  Nucleic Acids Res, 33, 3412-3423.
PDB codes: 2cvf 2cvh
15917243 T.Kinebuchi, W.Kagawa, H.Kurumizaka, and S.Yokoyama (2005).
Role of the N-terminal domain of the human DMC1 protein in octamer formation and DNA binding.
  J Biol Chem, 280, 28382-28387.  
15797011 T.Okada, and S.Keeney (2005).
Homologous recombination: needing to have my say.
  Curr Biol, 15, R200-R202.  
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.  
15296782 C.Wyman, and R.Kanaar (2004).
Homologous recombination: down to the wire.
  Curr Biol, 14, R629-R631.  
15192114 R.Enomoto, T.Kinebuchi, M.Sato, H.Yagi, T.Shibata, H.Kurumizaka, and S.Yokoyama (2004).
Positive role of the mammalian TBPIP/HOP2 protein in DMC1-mediated homologous pairing.
  J Biol Chem, 279, 35263-35272.  
15499584 S.Sauvageau, M.Ploquin, and J.Y.Masson (2004).
Exploring the multiple facets of the meiotic recombinase Dmc1.
  Bioessays, 26, 1151-1155.  
15330855 Y.Takizawa, T.Kinebuchi, W.Kagawa, S.Yokoyama, T.Shibata, and H.Kurumizaka (2004).
Mutational analyses of the human Rad51-Tyr315 residue, a site for phosphorylation in leukaemia cells.
  Genes Cells, 9, 781-790.  
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.