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protein dna_rna links
Transferase/DNA PDB id
1bdx
Jmol
Contents
Protein chains
190 a.a.* *
DNA/RNA
* Residue conservation analysis
* C-alpha coords only
PDB id:
1bdx
Name: Transferase/DNA
Title: E. Coli DNA helicase ruva with bound DNA holliday junction, alpha carbons and phosphate atoms only
Structure: DNA (5'- d(p Gp Cp Ap Tp Gp Cp Ap Tp Ap Tp Gp Cp Ap Tp Gp C)-3'). Chain: j, k, l, m. Engineered: yes. Holliday junction DNA helicase ruva. Chain: a, b, c, d. Engineered: yes
Source: Synthetic: yes. Escherichia coli bl21(de3). Organism_taxid: 469008. Strain: bl21. Variant: de3. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: de3.
Resolution:
6.00Å     R-factor:   not given    
Authors: D.Hargreaves,D.W.Rice,S.E.Sedelnikova,P.J.Artymiuk, R.G.Lloyd,J.B.Rafferty
Key ref: D.Hargreaves et al. (1998). Crystal structure of E.coli RuvA with bound DNA Holliday junction at 6 A resolution. Nat Struct Biol, 5, 441-446. PubMed id: 9628481 DOI: 10.1038/nsb0698-441
Date:
11-May-98     Release date:   24-Nov-99    
 Headers
 References

Protein chains
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

 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: 10.1038/nsb0698-441 Nat Struct Biol 5:441-446 (1998)
PubMed id: 9628481  
 
 
Crystal structure of E.coli RuvA with bound DNA Holliday junction at 6 A resolution.
D.Hargreaves, D.W.Rice, S.E.Sedelnikova, P.J.Artymiuk, R.G.Lloyd, J.B.Rafferty.
 
  ABSTRACT  
 
Here we present the crystal structure of the Escherichia coli protein RuvA bound to a key DNA intermediate in recombination, the Holliday junction. The structure, solved by isomorphous replacement and density modification at 6 A resolution, reveals the molecular architecture at the heart of the branch migration and resolution reactions required to process Holliday intermediates into recombinant DNA molecules. It also reveals directly for the first time the structure of the Holliday junction. A single RuvA tetramer is bound to one face of a junction whose four DNA duplex arms are arranged in an open and essentially four-fold symmetric conformation. Protein-DNA contacts are mediated by two copies of a helix-hairpin-helix motif per RuvA subunit that contact the phosphate backbone in a very similar manner. The open structure of the junction stabilized by RuvA binding exposes a DNA surface that could be bound by the RuvC endonuclease to promote resolution.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20094658 C.D.McGuinness, M.K.Nishimura, D.Keszenman-Pereyra, P.Dickinson, C.J.Campbell, T.T.Bachmann, P.Ghazal, and J.Crain (2010).
Detection of single nucleotide polymorphisms using a DNA Holliday junction nanoswitch--a high-throughput fluorescence lifetime assay.
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19406929 J.Atkinson, and P.McGlynn (2009).
Replication fork reversal and the maintenance of genome stability.
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19502410 M.Castellanos, and D.Romero (2009).
The extent of migration of the Holliday junction is a crucial factor for gene conversion in Rhizobium etli.
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18477633 D.Svozil, J.Kalina, M.Omelka, and B.Schneider (2008).
DNA conformations and their sequence preferences.
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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.  
18668125 K.Saikrishnan, S.P.Griffiths, N.Cook, R.Court, and D.B.Wigley (2008).
DNA binding to RecD: role of the 1B domain in SF1B helicase activity.
  EMBO J, 27, 2222-2229.
PDB codes: 3e1s 3k70
18658216 M.A.Karymov, M.Chinnaraj, A.Bogdanov, A.R.Srinivasan, G.Zheng, W.K.Olson, and Y.L.Lyubchenko (2008).
Structure, dynamics, and branch migration of a DNA Holliday junction: a single-molecule fluorescence and modeling study.
  Biophys J, 95, 4372-4383.  
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.  
17873859 C.Biertümpfel, W.Yang, and D.Suck (2007).
Crystal structure of T4 endonuclease VII resolving a Holliday junction.
  Nature, 449, 616-620.
PDB codes: 2qnc 2qnf
17873858 J.M.Hadden, A.C.Déclais, S.B.Carr, D.M.Lilley, and S.E.Phillips (2007).
The structural basis of Holliday junction resolution by T7 endonuclease I.
  Nature, 449, 621-624.
PDB code: 2pfj
17545145 O.M.Mazina, M.J.Rossi, N.H.Thomaä, and A.V.Mazin (2007).
Interactions of human rad54 protein with branched DNA molecules.
  J Biol Chem, 282, 21068-21080.  
16575941 P.A.Khuu, A.R.Voth, F.A.Hays, and P.S.Ho (2006).
The stacked-X DNA Holliday junction and protein recognition.
  J Mol Recognit, 19, 234-242.  
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.  
15720544 F.A.Curtis, P.Reed, and G.J.Sharples (2005).
Evolution of a phage RuvC endonuclease for resolution of both Holliday and branched DNA junctions.
  Mol Microbiol, 55, 1332-1345.  
16084380 G.D.Van Duyne (2005).
Bending and cutting forks and flaps.
  Structure, 13, 1092-1093.  
15828044 J.Malo, J.C.Mitchell, C.Vénien-Bryan, J.R.Harris, H.Wille, D.J.Sherratt, and A.J.Turberfield (2005).
Engineering a 2D protein-DNA crystal.
  Angew Chem Int Ed Engl, 44, 3057-3061.  
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
16076955 O.V.Tsodikov, J.H.Enzlin, O.D.Schärer, and T.Ellenberger (2005).
Crystal structure and DNA binding functions of ERCC1, a subunit of the DNA structure-specific endonuclease XPF-ERCC1.
  Proc Natl Acad Sci U S A, 102, 11236-11241.
PDB codes: 2a1i 2a1j
15292508 A.Dawid, V.Croquette, M.Grigoriev, and F.Heslot (2004).
Single-molecule study of RuvAB-mediated Holliday-junction migration.
  Proc Natl Acad Sci U S A, 101, 11611-11616.  
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.  
15065656 G.S.Briggs, A.A.Mahdi, G.R.Weller, Q.Wen, and R.G.Lloyd (2004).
Interplay between DNA replication, recombination and repair based on the structure of RecG helicase.
  Philos Trans R Soc Lond B Biol Sci, 359, 49-59.  
15173384 J.Watson, F.A.Hays, and P.S.Ho (2004).
Definitions and analysis of DNA Holliday junction geometry.
  Nucleic Acids Res, 32, 3017-3027.  
15281122 K.Nam, C.Honer, and C.Schumacher (2004).
Structural components of SCAN-domain dimerizations.
  Proteins, 56, 685-692.  
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.  
15520813 Y.Liu, and S.C.West (2004).
Happy Hollidays: 40th anniversary of the Holliday junction.
  Nat Rev Mol Cell Biol, 5, 937-944.  
14563836 F.A.Hays, J.Watson, and P.S.Ho (2003).
Caution! DNA crossing: crystal structures of Holliday junctions.
  J Biol Chem, 278, 49663-49666.  
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.  
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
12944465 R.E.Wellinger, P.Schär, and J.M.Sogo (2003).
Rad52-independent accumulation of joint circular minichromosomes during S phase in Saccharomyces cerevisiae.
  Mol Cell Biol, 23, 6363-6372.  
11788713 B.N.van Buuren, T.Hermann, S.S.Wijmenga, and E.Westhof (2002).
Brownian-dynamics simulations of metal-ion binding to four-way junctions.
  Nucleic Acids Res, 30, 507-514.  
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.  
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.  
11340053 G.D.Van Duyne (2001).
A structural view of cre-loxp site-specific recombination.
  Annu Rev Biophys Biomol Struct, 30, 87.  
11251805 G.J.Sharples (2001).
The X philes: structure-specific endonucleases that resolve Holliday junctions.
  Mol Microbiol, 39, 823-834.  
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
11551967 P.McGlynn, and R.G.Lloyd (2001).
Action of RuvAB at replication fork structures.
  J Biol Chem, 276, 41938-41944.  
11406378 P.S.Ho, and B.F.Eichman (2001).
The crystal structures of DNA Holliday junctions.
  Curr Opin Struct Biol, 11, 302-308.  
11726496 S.Ceschini, A.Keeley, M.S.McAlister, M.Oram, J.Phelan, L.H.Pearl, I.R.Tsaneva, and T.E.Barrett (2001).
Crystal structure of the fission yeast mitochondrial Holliday junction resolvase Ydc2.
  EMBO J, 20, 6601-6611.
PDB code: 1kcf
10760268 B.F.Eichman, J.M.Vargason, B.H.Mooers, and P.S.Ho (2000).
The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions.
  Proc Natl Acad Sci U S A, 97, 3971-3976.
PDB codes: 1dcv 1dcw
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.  
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
10908318 X.Shao, and N.V.Grishin (2000).
Common fold in helix-hairpin-helix proteins.
  Nucleic Acids Res, 28, 2643-2650.  
  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.  
10410797 C.D.Mol, S.S.Parikh, C.D.Putnam, T.P.Lo, and J.A.Tainer (1999).
DNA repair mechanisms for the recognition and removal of damaged DNA bases.
  Annu Rev Biophys Biomol Struct, 28, 101-128.  
10047575 D.N.Gopaul, and G.D.Duyne (1999).
Structure and mechanism in site-specific recombination.
  Curr Opin Struct Biol, 9, 14-20.  
  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.  
10052955 R.Sha, F.Liu, M.F.Bruist, and N.C.Seeman (1999).
Parallel helical domains in DNA branched junctions containing 5',5' and 3',3' linkages.
  Biochemistry, 38, 2832-2841.  
10464259 T.Hishida, H.Iwasaki, T.Yagi, and H.Shinagawa (1999).
Role of walker motif A of RuvB protein in promoting branch migration of holliday junctions. Walker motif a mutations affect Atp binding, Atp hydrolyzing, and DNA binding activities of Ruvb.
  J Biol Chem, 274, 25335-25342.  
9778254 D.J.Hosfield, C.D.Mol, B.Shen, and J.A.Tainer (1998).
Structure of the DNA repair and replication endonuclease and exonuclease FEN-1: coupling DNA and PCNA binding to FEN-1 activity.
  Cell, 95, 135-146.
PDB code: 1b43
9857040 M.C.Whitby, and J.Dixon (1998).
Substrate specificity of the SpCCE1 holliday junction resolvase of Schizosaccharomyces pombe.
  J Biol Chem, 273, 35063-35073.  
9774975 M.Grigoriev, and P.Hsieh (1998).
Migration of a Holliday junction through a nucleosome directed by the E. coli RuvAB motor protein.
  Mol Cell, 2, 373-381.  
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.  
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.