PDBsum entry 1hqc

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Hydrolase PDB id
Jmol PyMol
Protein chains
314 a.a. *
ADE ×2
_MG ×2
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structure of ruvb from thermus thermophilus hb8
Structure: Ruvb. Chain: a, b. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Gene: ruvb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Tetramer (from PQS)
3.20Å     R-factor:   0.263     R-free:   0.296
Authors: K.Yamada,N.Kunishima,K.Mayanagi,H.Iwasaki,K.Morikawa
Key ref:
K.Yamada et al. (2001). Crystal structure of the Holliday junction migration motor protein RuvB from Thermus thermophilus HB8. Proc Natl Acad Sci U S A, 98, 1442-1447. PubMed id: 11171970 DOI: 10.1073/pnas.031470598
15-Dec-00     Release date:   21-Feb-01    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q5SL87  (RUVB_THET8) -  Holliday junction ATP-dependent DNA helicase RuvB
324 a.a.
314 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Dna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
+ H(2)O
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     response to DNA damage stimulus   5 terms 
  Biochemical function     nucleotide binding     6 terms  


DOI no: 10.1073/pnas.031470598 Proc Natl Acad Sci U S A 98:1442-1447 (2001)
PubMed id: 11171970  
Crystal structure of the Holliday junction migration motor protein RuvB from Thermus thermophilus HB8.
K.Yamada, N.Kunishima, K.Mayanagi, T.Ohnishi, T.Nishino, H.Iwasaki, H.Shinagawa, K.Morikawa.
We report here the crystal structure of the RuvB motor protein from Thermus thermophilus HB8, which drives branch migration of the Holliday junction during homologous recombination. RuvB has a crescent-like architecture consisting of three consecutive domains, the first two of which are involved in ATP binding and hydrolysis. DNA is likely to interact with a large basic cleft, which encompasses the ATP-binding pocket and domain boundaries, whereas the junction-recognition protein RuvA may bind a flexible beta-hairpin protruding from the N-terminal domain. The structures of two subunits, related by a noncrystallographic pseudo-2-fold axis, imply that conformational changes of motor protein coupled with ATP hydrolysis may reflect motility essential for its translocation around double-stranded DNA.
  Selected figure(s)  
Figure 2.
Fig. 2. Electron density maps and ribbon models of nucleotide-binding sites in the two ncs subunits. Possible residues that interact with nucleotides are depicted: Y14, I15, Y168, R179, and D180 are in contact with the adenine bases; K51 and T52 (Walker A), D97 (Walker B), T146 (Sensor I), and R205 (Sensor II) may interact with the phosphate groups. The stick models of (a) AMPPNP and (b) ADP were represented with corresponding simulated annealed F[o] F[c] omit maps at a 1.5 contour. The nucleotide atoms were omitted from the map calculation. Ribbons corresponding to the two sensor motifs and the two Walker motifs are indicated by the same color as in Fig. 1c. (c) Structural differences between the "A" (blue) and "B" (yellow) forms. Here, only the C backbones of domain N (ATPase domain) were superimposed between the two ncs molecules.
Figure 4.
Fig. 4. Comparison of the hypothetical hexamer model of RuvB with the electron microscopic image. (a) Projection image (Left) of negative stained RuvB complexed with a 30-bp DNA, obtained by averaging 140 top views in our previous work (15). The resolution of the averaged image was 30.0 Å. The top views of the hexamer model (Center and Right) were constructed by superimposing each ATPase domain of RuvB (AMPPNP form) (blue region) onto the corresponding regions of HslU crystal structure (25) and the NSF crystal structure (23), respectively. The domains N, M, C, labeled residues, and the bound nucleotides are represented with the same color code as defined in Fig. 1. (b) Projection image (Left) of RuvB-DNA obtained by averaging 266 side views. This image of the single ring was taken from one-half of the double ring, which encircles duplex DNA. The resolution of the averaged image was 34.3 Å. Side view of the hexamer model (Right). [Reproduced with permission from ref. 15 (Copyright 2000, Academic Press).
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  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.  
18466635 J.Snider, G.Thibault, and W.A.Houry (2008).
The AAA+ superfamily of functionally diverse proteins.
  Genome Biol, 9, 216.  
18446235 M.Proell, S.J.Riedl, J.H.Fritz, A.M.Rojas, and R.Schwarzenbacher (2008).
The Nod-like receptor (NLR) family: a tale of similarities and differences.
  PLoS ONE, 3, e2119.  
  18765919 S.Gorynia, P.M.Matias, T.M.Bandeiras, P.Donner, and M.A.Carrondo (2008).
Cloning, expression, purification, crystallization and preliminary X-ray analysis of the human RuvBL1-RuvBL2 complex.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 840-846.  
17506634 M.R.Singleton, M.S.Dillingham, and D.B.Wigley (2007).
Structure and mechanism of helicases and nucleic acid translocases.
  Annu Rev Biochem, 76, 23-50.  
17157497 M.Rappas, D.Bose, and X.Zhang (2007).
Bacterial enhancer-binding proteins: unlocking sigma54-dependent gene transcription.
  Curr Opin Struct Biol, 17, 110-116.  
17121997 A.W.Serohijos, Y.Chen, F.Ding, T.C.Elston, and N.V.Dokholyan (2006).
A structural model reveals energy transduction in dynein.
  Proc Natl Acad Sci U S A, 103, 18540-18545.
PDB code: 2gf8
16322571 T.Yamamoto, T.Matsuda, T.Inoue, H.Matsumura, M.Morikawa, S.Kanaya, and Y.Kai (2006).
Crystal structure of TBP-interacting protein (Tk-TIP26) and implications for its inhibition mechanism of the interaction between TBP and TATA-DNA.
  Protein Sci, 15, 152-161.
PDB code: 2czr
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.  
15642269 T.Nishino, K.Komori, D.Tsuchiya, Y.Ishino, and K.Morikawa (2005).
Crystal structure and functional implications of Pyrococcus furiosus hef helicase domain involved in branched DNA processing.
  Structure, 13, 143-153.
PDB code: 1wp9
15359274 D.J.Fitzgerald, C.DeLuca, I.Berger, H.Gaillard, R.Sigrist, K.Schimmele, and T.J.Richmond (2004).
Reaction cycle of the yeast Isw2 chromatin remodeling complex.
  EMBO J, 23, 3836-3843.  
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.  
15128295 N.Tuteja, and R.Tuteja (2004).
Unraveling DNA helicases. Motif, structure, mechanism and function.
  Eur J Biochem, 271, 1849-1863.  
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.  
12622725 F.Hayashi, H.Suzuki, R.Iwase, T.Uzumaki, A.Miyake, J.R.Shen, K.Imada, Y.Furukawa, K.Yonekura, K.Namba, and M.Ishiura (2003).
ATP-induced hexameric ring structure of the cyanobacterial circadian clock protein KaiC.
  Genes Cells, 8, 287-296.  
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.  
14561776 S.Y.Lee, A.De La Torre, D.Yan, S.Kustu, B.T.Nixon, and D.E.Wemmer (2003).
Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains.
  Genes Dev, 17, 2552-2563.
PDB codes: 1ny5 1ny6
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.  
12377127 H.Niwa, D.Tsuchiya, H.Makyio, M.Yoshida, and K.Morikawa (2002).
Hexameric ring structure of the ATPase domain of the membrane-integrated metalloprotease FtsH from Thermus thermophilus HB8.
  Structure, 10, 1415-1423.
PDB codes: 1ixz 1iy0 1iy1 1iy2
11839499 J.M.Caruthers, and D.B.McKay (2002).
Helicase structure and mechanism.
  Curr Opin Struct Biol, 12, 123-133.  
12234917 J.P.Erzberger, M.M.Pirruccello, and J.M.Berger (2002).
The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation.
  EMBO J, 21, 4763-4773.
PDB code: 1l8q
11889086 M.R.Singleton, and D.B.Wigley (2002).
Modularity and specialization in superfamily 1 and 2 helicases.
  J Bacteriol, 184, 1819-1826.  
12180911 X.Zhang, M.Chaney, S.R.Wigneshweraraj, J.Schumacher, P.Bordes, W.Cannon, and M.Buck (2002).
Mechanochemical ATPases and transcriptional activation.
  Mol Microbiol, 45, 895-903.  
11709174 J.Wang, J.J.Song, I.S.Seong, M.C.Franklin, S.Kamtekar, S.H.Eom, and C.H.Chung (2001).
Nucleotide-dependent conformational changes in a protease-associated ATPase HsIU.
  Structure, 9, 1107-1116.
PDB codes: 1hqy 1ht1 1ht2
11595187 M.R.Singleton, S.Scaife, and D.B.Wigley (2001).
Structural analysis of DNA replication fork reversal by RecG.
  Cell, 107, 79-89.
PDB code: 1gm5
11473577 T.Ogura, and A.J.Wilkinson (2001).
AAA+ superfamily ATPases: common structure--diverse function.
  Genes Cells, 6, 575-597.  
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.