PDBsum entry 1ixs

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Hydrolase PDB id
Protein chains
50 a.a.
315 a.a. *
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structure of ruvb complexed with ruva domain iii
Structure: Holliday junction DNA helicase ruva. Chain: a. Fragment: ruva domain iii. Engineered: yes. Ruvb. Chain: b. Fragment: residues 1-318. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Gene: ruva. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: ruvb.
Biol. unit: Dimer (from PQS)
3.20Å     R-factor:   0.231     R-free:   0.294
Authors: K.Yamada,T.Miyata,D.Tsuchiya,T.Oyama,Y.Fujiwara,T.Ohnishi, H.Iwasaki,H.Shinagawa,M.Ariyoshi,K.Mayanagi,K.Morikawa
Key ref:
K.Yamada et al. (2002). Crystal structure of the RuvA-RuvB complex: a structural basis for the Holliday junction migrating motor machinery. Mol Cell, 10, 671-681. PubMed id: 12408833 DOI: 10.1016/S1097-2765(02)00641-X
04-Jul-02     Release date:   06-Nov-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9F1Q3  (RUVA_THET8) -  Holliday junction ATP-dependent DNA helicase RuvA
191 a.a.
50 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SL87  (RUVB_THET8) -  Holliday junction ATP-dependent DNA helicase RuvB
324 a.a.
315 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.  - Dna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
+ H(2)O
Bound ligand (Het Group name = ANP)
matches with 81.00% similarity
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     Holliday junction helicase complex   1 term 
  Biological process     response to DNA damage stimulus   5 terms 
  Biochemical function     nucleotide binding     7 terms  


DOI no: 10.1016/S1097-2765(02)00641-X Mol Cell 10:671-681 (2002)
PubMed id: 12408833  
Crystal structure of the RuvA-RuvB complex: a structural basis for the Holliday junction migrating motor machinery.
K.Yamada, T.Miyata, D.Tsuchiya, T.Oyama, Y.Fujiwara, T.Ohnishi, H.Iwasaki, H.Shinagawa, M.Ariyoshi, K.Mayanagi, K.Morikawa.
We present the X-ray structure of the RuvA-RuvB complex, which plays a crucial role in ATP-dependent branch migration. Two RuvA tetramers form the symmetric and closed octameric shell, where four RuvA domain IIIs spring out in the two opposite directions to be individually caught by a single RuvB. The binding of domain III deforms the protruding beta hairpin in the N-terminal domain of RuvB and thereby appears to induce a functional and less symmetric RuvB hexameric ring. The model of the RuvA-RuvB junction DNA ternary complex, constructed by fitting the X-ray structure into the averaged electron microscopic images of the RuvA-RuvB junction, appears to be more compatible with the branch migration mode of a fixed RuvA-RuvB interaction than with a rotational interaction mode.
  Selected figure(s)  
Figure 4.
Figure 4. Averaged Electron Microscopic Image of the RuvA-RuvB-Holliday Junction Ternary Complex and the Corresponding Functional Atomic ModelThe IMAGIC program package (van Heel et al., 1996) was used to cluster particle images and to obtain class averages. The hypothetical model was constructed by fitting the RuvA octameric core structure (yellow) and the RuvB hexamer models (blue) into the averaged images, referring to the hexameric oligomerization of the HslU protein similar to RuvB (Sousa et al., 2000). One pair of subunits related in each hexameric ring by the central 2-fold axis was replaced by the two domain III (orange)-RuvB (magenta) complexes (see text). Averaged electron microscopic images correspond to two orthogonal views of the ternary complex. The 858 original images were grouped into three major classes of averaged images, and only two of them, (A) and (B), averaged from 171 and 370 electron microscopic images, are shown here. Note the good coincidence of the images with the side (A) and end views (B) of the RuvA octameric core structure. The resolutions of the averaged images of (A) and (B) were estimated at 34 and 31 Å, respectively, from differential phase residuals. The scale bar represents 100 Å.
Figure 5.
Figure 5. Model of the Loading Process of the RuvA-RuvB Complex on a Holliday JunctionEach of the three components in this process was determined by X-ray analyses (forms I, II, and III) or by an electron microscopic study (form IV). The RuvA core region and domain III are colored by yellow and orange, respectively. The RuvB subunit is depicted by a blue oval. Red-trimmed ovals represent domain III bound to the RuvB subunit. The RuvA-RuvB complex (form III) is regarded as the preloading complex before forming the functional complex on a Holliday junction (form IV). During the conversion from form III to IV, the RuvB subunit that was previously connected with the RuvA octameric core is no longer replaced by other partners.
  The above figures are reprinted by permission from Cell Press: Mol Cell (2002, 10, 671-681) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21330489 A.P.Carter, C.Cho, L.Jin, and R.D.Vale (2011).
Crystal structure of the dynein motor domain.
  Science, 331, 1159-1165.
PDB code: 3qmz
  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.  
19406929 J.Atkinson, and P.McGlynn (2009).
Replication fork reversal and the maintenance of genome stability.
  Nucleic Acids Res, 37, 3475-3492.  
19486295 P.C.Burrows, J.Schumacher, S.Amartey, T.Ghosh, T.A.Burgis, X.Zhang, B.T.Nixon, and M.Buck (2009).
Functional roles of the pre-sensor I insertion sequence in an AAA+ bacterial enhancer binding protein.
  Mol Microbiol, 73, 519-533.  
19089981 Q.Xu, C.L.Rife, D.Carlton, M.D.Miller, S.S.Krishna, M.A.Elsliger, P.Abdubek, T.Astakhova, H.J.Chiu, T.Clayton, L.Duan, J.Feuerhelm, S.K.Grzechnik, J.Hale, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, A.Kumar, D.McMullan, A.T.Morse, E.Nigoghossian, L.Okach, S.Oommachen, J.Paulsen, R.Reyes, H.van den Bedem, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2009).
Crystal structure of a novel archaeal AAA+ ATPase SSO1545 from Sulfolobus solfataricus.
  Proteins, 74, 1041-1049.
PDB code: 2fna
18579587 A.Kumar, W.S.Joo, G.Meinke, S.Moine, E.N.Naumova, and P.A.Bullock (2008).
Evidence for a structural relationship between BRCT domains and the helicase domains of the replication initiators encoded by the Polyomaviridae and Papillomaviridae families of DNA tumor viruses.
  J Virol, 82, 8849-8862.  
19073923 A.S.Brewster, G.Wang, X.Yu, W.B.Greenleaf, J.M.Carazo, M.Tjajadia, M.G.Klein, and X.S.Chen (2008).
Crystal structure of a near-full-length archaeal MCM: functional insights for an AAA+ hexameric helicase.
  Proc Natl Acad Sci U S A, 105, 20191-20196.
PDB code: 3f9v
18940606 E.Torreira, S.Jha, J.R.López-Blanco, E.Arias-Palomo, P.Chacón, C.Cañas, S.Ayora, A.Dutta, and O.Llorca (2008).
Architecture of the pontin/reptin complex, essential in the assembly of several macromolecular complexes.
  Structure, 16, 1511-1520.  
18931785 I.J.Finkelstein, and E.C.Greene (2008).
Single molecule studies of homologous recombination.
  Mol Biosyst, 4, 1094-1104.  
18466635 J.Snider, G.Thibault, and W.A.Houry (2008).
The AAA+ superfamily of functionally diverse proteins.
  Genome Biol, 9, 216.  
18942176 M.Le Masson, Z.Baharoglu, and B.Michel (2008).
ruvA and ruvB mutants specifically impaired for replication fork reversal.
  Mol Microbiol, 70, 537-548.  
18369438 Z.Baharoglu, A.S.Bradley, M.Le Masson, I.Tsaneva, and B.Michel (2008).
ruvA Mutants that resolve Holliday junctions but do not reverse replication forks.
  PLoS Genet, 4, e1000012.  
17599913 I.Tato, I.Matilla, I.Arechaga, S.Zunzunegui, la Cruz, and E.Cabezon (2007).
The ATPase activity of the DNA transporter TrwB is modulated by protein TrwA: implications for a common assembly mechanism of DNA translocating motors.
  J Biol Chem, 282, 25569-25576.  
17157498 K.P.Hopfner, and J.Michaelis (2007).
Mechanisms of nucleic acid translocases: lessons from structural biology and single-molecule biophysics.
  Curr Opin Struct Biol, 17, 87-95.  
17062628 A.Costa, T.Pape, M.van Heel, P.Brick, A.Patwardhan, and S.Onesti (2006).
Structural basis of the Methanothermobacter thermautotrophicus MCM helicase activity.
  Nucleic Acids Res, 34, 5829-5838.  
16689629 J.P.Erzberger, and J.M.Berger (2006).
Evolutionary relationships and structural mechanisms of AAA+ proteins.
  Annu Rev Biophys Biomol Struct, 35, 93.  
  16880543 J.R.Prabu, S.Thamotharan, J.S.Khanduja, E.Z.Alipio, C.Y.Kim, G.S.Waldo, T.C.Terwilliger, B.Segelke, T.Lekin, D.Toppani, L.W.Hung, M.Yu, E.Bursey, K.Muniyappa, N.R.Chandra, and M.Vijayan (2006).
Structure of Mycobacterium tuberculosis RuvA, a protein involved in recombination.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 731-734.
PDB code: 2h5x
16864792 Y.W.Han, T.Tani, M.Hayashi, T.Hishida, H.Iwasaki, H.Shinagawa, and Y.Harada (2006).
Direct observation of DNA rotation during branch migration of Holliday junction DNA by Escherichia coli RuvA-RuvB protein complex.
  Proc Natl Acad Sci U S A, 103, 11544-11548.  
15556943 C.V.Privezentzev, A.Keeley, B.Sigala, and I.R.Tsaneva (2005).
The role of RuvA octamerization for RuvAB function in vitro and in vivo.
  J Biol Chem, 280, 3365-3375.  
15867153 K.V.Kepple, J.L.Boldt, and A.M.Segall (2005).
Holliday junction-binding peptides inhibit distinct junction-processing enzymes.
  Proc Natl Acad Sci U S A, 102, 6867-6872.  
15808743 L.Aravind, V.Anantharaman, S.Balaji, M.M.Babu, and L.M.Iyer (2005).
The many faces of the helix-turn-helix domain: transcription regulation and beyond.
  FEMS Microbiol Rev, 29, 231-262.  
15972826 T.Ohnishi, T.Hishida, Y.Harada, H.Iwasaki, and H.Shinagawa (2005).
Structure-function analysis of the three domains of RuvB DNA motor protein.
  J Biol Chem, 280, 30504-30510.  
15670210 T.Tsurimoto, A.Shinozaki, M.Yano, M.Seki, and T.Enomoto (2005).
Human Werner helicase interacting protein 1 (WRNIP1) functions as a novel modulator for DNA polymerase delta.
  Genes Cells, 10, 13-22.  
15167893 C.Dennis, A.Fedorov, E.Käs, L.Salomé, and M.Grigoriev (2004).
RuvAB-directed branch migration of individual Holliday junctions is impeded by sequence heterology.
  EMBO J, 23, 2413-2422.  
15093826 K.Yamada, M.Ariyoshi, and K.Morikawa (2004).
Three-dimensional structural views of branch migration and resolution in DNA homologous recombination.
  Curr Opin Struct Biol, 14, 130-137.  
15292509 R.Amit, O.Gileadi, and J.Stavans (2004).
Direct observation of RuvAB-catalyzed branch migration of single Holliday junctions.
  Proc Natl Acad Sci U S A, 101, 11605-11610.  
15210950 T.Hishida, Y.W.Han, S.Fujimoto, H.Iwasaki, and H.Shinagawa (2004).
Direct evidence that a conserved arginine in RuvB AAA+ ATPase acts as an allosteric effector for the ATPase activity of the adjacent subunit in a hexamer.
  Proc Natl Acad Sci U S A, 101, 9573-9577.  
15520813 Y.Liu, and S.C.West (2004).
Happy Hollidays: 40th anniversary of the Holliday junction.
  Nat Rev Mol Cell Biol, 5, 937-944.  
12441335 H.Yokoyama, H.Kurumizaka, S.Ikawa, S.Yokoyama, and T.Shibata (2003).
Holliday junction binding activity of the human Rad51B protein.
  J Biol Chem, 278, 2767-2772.  
12906833 J.A.James, C.R.Escalante, M.Yoon-Robarts, T.A.Edwards, R.M.Linden, and A.K.Aggarwal (2003).
Crystal structure of the SF3 helicase from adeno-associated virus type 2.
  Structure, 11, 1025-1035.
PDB code: 1s9h
12778123 S.C.West (2003).
Molecular views of recombination proteins and their control.
  Nat Rev Mol Cell Biol, 4, 435-445.  
12940820 T.Hishida, H.Iwasaki, Y.W.Han, T.Ohnishi, and H.Shinagawa (2003).
Uncoupling of the ATPase activity from the branch migration activity of RuvAB protein complexes containing both wild-type and ATPase-defective RuvB proteins.
  Genes Cells, 8, 721-730.  
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.