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Helicase PDB id
1cuk
Jmol
Contents
Protein chain
190 a.a. *
Waters ×51
* Residue conservation analysis
PDB id:
1cuk
Name: Helicase
Title: Escherichia coli ruva protein at ph 4.9 and room temperature
Structure: Ruva protein. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: 12 bl21 (de3). Cell_line: bl21. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
1.90Å     R-factor:   0.209    
Authors: J.B.Rafferty,D.W.Rice
Key ref:
J.B.Rafferty et al. (1996). Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction. Science, 274, 415-421. PubMed id: 8832889 DOI: 10.1126/science.274.5286.415
Date:
28-Aug-96     Release date:   22-Oct-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A809  (RUVA_ECOLI) -  Holliday junction ATP-dependent DNA helicase RuvA
Seq:
Struc: 		203 a.a.
190 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.3.6.4.12  - Dna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
ATP
 + H(2)O
 = ADP
 + 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   4 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
    reference    
 
 
DOI no: 10.1126/science.274.5286.415 Science 274:415-421 (1996)
PubMed id: 8832889  
 
 
Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction.
J.B.Rafferty, S.E.Sedelnikova, D.Hargreaves, P.J.Artymiuk, P.J.Baker, G.J.Sharples, A.A.Mahdi, R.G.Lloyd, D.W.Rice.
 
  ABSTRACT  
 
The Escherichia coli DNA binding protein RuvA acts in concert with the helicase RuvB to drive branch migration of Holliday intermediates during recombination and DNA repair. The atomic structure of RuvA was determined at a resolution of 1.9 angstroms. Four monomers of RuvA are related by fourfold symmetry in a manner reminiscent of a four-petaled flower. The four DNA duplex arms of a Holliday junction can be modeled in a square planar configuration and docked into grooves on the concave surface of the protein around a central pin that may facilitate strand separation during the migration reaction. The model presented reveals how a RuvAB-junction complex may also accommodate the resolvase RuvC.
 
  Selected figure(s)  
 
Figure 2.
Rg. 2 Representations of the structure of RwA. 		Figure 3.
Fig. 3. Representations of RuvA and Holliday junction protein complexes.
 
  The above figures are reprinted by permission from the AAAs: Science (1996, 274, 415-421) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20826342 F.Wang, Y.Yang, T.R.Singh, V.Busygina, R.Guo, K.Wan, W.Wang, P.Sung, A.R.Meetei, and M.Lei (2010).
Crystal structures of RMI1 and RMI2, two OB-fold regulatory subunits of the BLM complex.
  Structure, 18, 1159-1170.
PDB codes: 3nbh 3nbi
19406929 J.Atkinson, and P.McGlynn (2009).
Replication fork reversal and the maintenance of genome stability.
  Nucleic Acids Res, 37, 3475-3492.  
19666720 P.Lagerbäck, E.Andersson, C.Malmberg, and K.Carlson (2009).
Bacteriophage T4 endonuclease II, a promiscuous GIY-YIG nuclease, binds as a tetramer to two DNA substrates.
  Nucleic Acids Res, 37, 6174-6183.  
18755052 D.M.Lilley (2008).
Analysis of branched nucleic acid structure using comparative gel electrophoresis.
  Q Rev Biophys, 41, 1.  
18439896 G.Witte, S.Hartung, K.Büttner, and K.P.Hopfner (2008).
Structural biochemistry of a bacterial checkpoint protein reveals diadenylate cyclase activity regulated by DNA recombination intermediates.
  Mol Cell, 30, 167-178.
PDB codes: 3c1y 3c1z 3c21 3c23
18986999 J.A.Buss, Y.Kimura, and P.R.Bianco (2008).
RecG interacts directly with SSB: implications for stalled replication fork regression.
  Nucleic Acids Res, 36, 7029-7042.  
19052323 M.S.Dillingham, and S.C.Kowalczykowski (2008).
RecBCD enzyme and the repair of double-stranded DNA breaks.
  Microbiol Mol Biol Rev, 72, 642.  
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.  
16641988 D.MacDonald, G.Demarre, M.Bouvier, D.Mazel, and D.N.Gopaul (2006).
Structural basis for broad DNA-specificity in integron recombination.
  Nature, 440, 1157-1162.
PDB code: 2a3v
  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
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.  
15719018 M.Newman, J.Murray-Rust, J.Lally, J.Rudolf, A.Fadden, P.P.Knowles, M.F.White, and N.Q.McDonald (2005).
Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition.
  EMBO J, 24, 895-905.
PDB codes: 2bgw 2bhn
16154091 N.McGregor, S.Ayora, S.Sedelnikova, B.Carrasco, J.C.Alonso, P.Thaw, and J.Rafferty (2005).
The structure of Bacillus subtilis RecU Holliday junction resolvase and its role in substrate selection and sequence-specific cleavage.
  Structure, 13, 1341-1351.
PDB code: 1zp7
15014443 A.Irimia, D.Madern, G.Zaccaï, and F.M.Vellieux (2004).
Methanoarchaeal sulfolactate dehydrogenase: prototype of a new family of NADH-dependent enzymes.
  EMBO J, 23, 1234-1244.
PDB codes: 1rfm 2x06
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.  
15111420 M.Nöllmann, W.M.Stark, and O.Byron (2004).
Low-resolution reconstruction of a synthetic DNA holliday junction.
  Biophys J, 86, 3060-3069.  
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.  
12820967 J.B.Green, C.D.Gardner, R.P.Wharton, and A.K.Aggarwal (2003).
RNA recognition via the SAM domain of Smaug.
  Mol Cell, 11, 1537-1548.
PDB code: 1oxj
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.  
14506706 W.Gartner, J.Rossbacher, B.Zierhut, T.Daneva, W.Base, M.Weissel, W.Waldhäusl, M.S.Pasternack, and L.Wagner (2003).
The ATP-dependent helicase RUVBL1/TIP49a associates with tubulin during mitosis.
  Cell Motil Cytoskeleton, 56, 79-93.  
12423347 M.J.Dickman, S.M.Ingleston, S.E.Sedelnikova, J.B.Rafferty, R.G.Lloyd, J.A.Grasby, and D.P.Hornby (2002).
The RuvABC resolvasome.
  Eur J Biochem, 269, 5492-5501.  
11889086 M.R.Singleton, and D.B.Wigley (2002).
Modularity and specialization in superfamily 1 and 2 helicases.
  J Bacteriol, 184, 1819-1826.  
11874468 S.M.Ingleston, M.J.Dickman, J.A.Grasby, D.P.Hornby, G.J.Sharples, and R.G.Lloyd (2002).
Holliday junction binding and processing by the RuvA protein of Mycoplasma pneumoniae.
  Eur J Biochem, 269, 1525-1533.  
12426397 S.Singh, G.E.Folkers, A.M.Bonvin, R.Boelens, R.Wechselberger, A.Niztayev, and R.Kaptein (2002).
Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli.
  EMBO J, 21, 6257-6266.
PDB code: 1kft
11331763 C.S.Bond, M.Kvaratskhelia, D.Richard, M.F.White, and W.N.Hunter (2001).
Structure of Hjc, a Holliday junction resolvase, from Sulfolobus solfataricus.
  Proc Natl Acad Sci U S A, 98, 5509-5514.
PDB code: 1hh1
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
11782293 V.Agrawal, and R.K.Kishan (2001).
Functional evolution of two subtly different (similar) folds.
  BMC Struct Biol, 1, 5.  
11058099 A.J.Doherty, and S.W.Suh (2000).
Structural and mechanistic conservation in DNA ligases.
  Nucleic Acids Res, 28, 4051-4058.  
10662672 H.George, I.Kuraoka, D.A.Nauman, W.R.Kobertz, R.D.Wood, and S.C.West (2000).
RuvAB-mediated branch migration does not involve extensive DNA opening within the RuvB hexamer.
  Curr Biol, 10, 103-106.  
11163206 K.P.Lemon, and A.D.Grossman (2000).
Movement of replicating DNA through a stationary replisome.
  Mol Cell, 6, 1321-1330.  
10890893 M.Ariyoshi, T.Nishino, H.Iwasaki, H.Shinagawa, and K.Morikawa (2000).
Crystal structure of the holliday junction DNA in complex with a single RuvA tetramer.
  Proc Natl Acad Sci U S A, 97, 8257-8262.
PDB code: 1c7y
11031286 M.E.Wall, S.C.Gallagher, and J.Trewhella (2000).
Large-scale shape changes in proteins and macromolecular complexes.
  Annu Rev Phys Chem, 51, 355-380.  
11080172 S.M.Ingleston, G.J.Sharples, and R.G.Lloyd (2000).
The acidic pin of RuvA modulates Holliday junction binding and processing by the RuvABC resolvasome.
  EMBO J, 19, 6266-6274.  
10924106 T.C.Umland, S.Q.Wei, R.Craigie, and D.R.Davies (2000).
Structural basis of DNA bridging by barrier-to-autointegration factor.
  Biochemistry, 39, 9130-9138.
PDB code: 1ci4
11245216 T.Ohnishi, H.Iwasaki, Y.Ishino, S.Kuramitsu, A.Nakata, and H.Shinagawa (2000).
Identification and characterization of Thermus thermophilus HB8 RuvA protein, the subunit of the RuvAB protein complex that promotes branch migration of Holliday junctions.
  Genes Genet Syst, 75, 233-243.  
  10421637 A.J.van Gool, N.M.Hajibagheri, A.Stasiak, and S.C.West (1999).
Assembly of the Escherichia coli RuvABC resolvasome directs the orientation of holliday junction resolution.
  Genes Dev, 13, 1861-1870.  
  10585965 A.Kuzminov (1999).
Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda.
  Microbiol Mol Biol Rev, 63, 751.  
10089419 D.Hargreaves, J.B.Rafferty, S.E.Sedelnikova, R.G.Lloyd, and D.W.Rice (1999).
Crystallization of Escherichia coli RuvA complexed with a synthetic Holliday junction.
  Acta Crystallogr D Biol Crystallogr, 55, 263-265.  
  10482492 G.J.Sharples, S.M.Ingleston, and R.G.Lloyd (1999).
Holliday junction processing in bacteria: insights from the evolutionary conservation of RuvABC, RecG, and RusA.
  J Bacteriol, 181, 5543-5550.  
  10548040 M.Smalla, P.Schmieder, M.Kelly, A.Ter Laak, G.Krause, L.Ball, M.Wahl, P.Bork, and H.Oschkinat (1999).
Solution structure of the receptor tyrosine kinase EphB2 SAM domain and identification of two distinct homotypic interaction sites.
  Protein Sci, 8, 1954-1961.
PDB code: 1sgg
9637927 A.A.Davies, and S.C.West (1998).
Formation of RuvABC-Holliday junction complexes in vitro.
  Curr Biol, 8, 725-727.  
9501105 A.J.van Gool, R.Shah, C.Mézard, and S.C.West (1998).
Functional interactions between the holliday junction resolvase and the branch migration motor of Escherichia coli.
  EMBO J, 17, 1838-1845.  
9628481 D.Hargreaves, D.W.Rice, S.E.Sedelnikova, P.J.Artymiuk, R.G.Lloyd, and J.B.Rafferty (1998).
Crystal structure of E.coli RuvA with bound DNA Holliday junction at 6 A resolution.
  Nat Struct Biol, 5, 441-446.
PDB code: 1bdx
  9751641 D.P.Hornby, and G.C.Ford (1998).
Protein-mediated base flipping.
  Curr Opin Biotechnol, 9, 354-358.  
9813108 K.Ichiyanagi, H.Iwasaki, T.Hishida, and H.Shinagawa (1998).
Mutational analysis on structure-function relationship of a holliday junction specific endonuclease RuvC.
  Genes Cells, 3, 575-586.  
9814711 M.Seigneur, V.Bidnenko, S.D.Ehrlich, and B.Michel (1998).
RuvAB acts at arrested replication forks.
  Cell, 95, 419-430.  
9753317 S.C.West (1998).
RuvA gets X-rayed on holliday.
  Cell, 94, 699-701.  
9774974 S.M.Roe, T.Barlow, T.Brown, M.Oram, A.Keeley, I.R.Tsaneva, and L.H.Pearl (1998).
Crystal structure of an octameric RuvA-Holliday junction complex.
  Mol Cell, 2, 361-372.
PDB code: 1bvs
9512524 S.N.Chan, S.D.Vincent, and R.G.Lloyd (1998).
Recognition and manipulation of branched DNA by the RusA Holliday junction resolvase of Escherichia coli.
  Nucleic Acids Res, 26, 1560-1566.  
  9493263 T.Nishino, M.Ariyoshi, H.Iwasaki, H.Shinagawa, and K.Morikawa (1998).
Functional analyses of the domain structure in the Holliday junction binding protein RuvA.
  Structure, 6, 11-21.
PDB code: 1hjp
9751721 Y.Guo, and J.D.Gralla (1998).
Promoter opening via a DNA fork junction binding activity.
  Proc Natl Acad Sci U S A, 95, 11655-11660.  
9881170 Z.Wang, P.Yang, B.Fan, and Z.Chen (1998).
An oligo selection procedure for identification of sequence-specific DNA-binding activities associated with the plant defence response.
  Plant J, 16, 515-522.  
9380511 A.A.Mahdi, P.McGlynn, S.D.Levett, and R.G.Lloyd (1997).
DNA binding and helicase domains of the Escherichia coli recombination protein RecG.
  Nucleic Acids Res, 25, 3875-3880.  
9160752 A.K.Eggleston, A.H.Mitchell, and S.C.West (1997).
In vitro reconstitution of the late steps of genetic recombination in E. coli.
  Cell, 89, 607-617.  
9204276 A.Lebrun, and R.Lavery (1997).
Unusual DNA conformations.
  Curr Opin Struct Biol, 7, 348-354.  
  9375249 D.M.Lilley (1997).
Site-specific recombination caught in the act.
  Chem Biol, 4, 717-720.  
9434898 D.W.Rice, J.B.Rafferty, P.J.Artymiuk, and R.G.Lloyd (1997).
Insights into the mechanisms of homologous recombination from the structure of RuvA.
  Curr Opin Struct Biol, 7, 798-803.  
9370369 F.J.Overmars, V.Lanzotti, A.Galeone, A.Pepe, L.Mayol, J.A.Pikkemaat, and C.Altona (1997).
Design and NMR study of an immobile DNA four-way junction containing 38 nucleotides.
  Eur J Biochem, 249, 576-583.  
9008164 M.Bycroft, T.J.Hubbard, M.Proctor, S.M.Freund, and A.G.Murzin (1997).
The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold.
  Cell, 88, 235-242.
PDB code: 1sro
9287163 M.R.Sawaya, R.Prasad, S.H.Wilson, J.Kraut, and H.Pelletier (1997).
Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.
  Biochemistry, 36, 11205-11215.
PDB codes: 1bpx 1bpy 1bpz
9368738 N.D.Grindley (1997).
Site-specific recombination: synapsis and strand exchange revealed.
  Curr Biol, 7, R608-R612.  
9442895 S.C.West (1997).
Processing of recombination intermediates by the RuvABC proteins.
  Annu Rev Genet, 31, 213-244.  
9100019 X.Li, H.Wang, and N.C.Seeman (1997).
Direct evidence for Holliday junction crossover isomerization.
  Biochemistry, 36, 4240-4247.  
8946847 D.M.Lilley (1996).
A critical junction for RuvA.
  Nat Struct Biol, 3, 984-986.  
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.