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Gene regulation PDB id
1d8l
Jmol
Contents
Protein chains
140 a.a. *
Waters ×22
* Residue conservation analysis
PDB id:
1d8l
Name: Gene regulation
Title: E. Coli holliday junction binding protein ruva nh2 region lacking domain iii
Structure: Protein (holliday junction DNA helicase ruva). Chain: a, b. Fragment: nh2 region. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.50Å     R-factor:   0.247     R-free:   0.320
Authors: T.Nishino,H.Iwasaki,M.Kataoka,M.Ariyoshi,T.Fujita, H.Shinagawa,K.Morikawa
Key ref:
T.Nishino et al. (2000). Modulation of RuvB function by the mobile domain III of the Holliday junction recognition protein RuvA. J Mol Biol, 298, 407-416. PubMed id: 10772859 DOI: 10.1006/jmbi.2000.3675
Date:
25-Oct-99     Release date:   03-May-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A809  (RUVA_ECOLI) -  Holliday junction ATP-dependent DNA helicase RuvA
Seq:
Struc: 		203 a.a.
140 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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!
  Biological process     DNA repair   2 terms 
  Biochemical function     DNA binding     4 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2000.3675 J Mol Biol 298:407-416 (2000)
PubMed id: 10772859  
 
 
Modulation of RuvB function by the mobile domain III of the Holliday junction recognition protein RuvA.
T.Nishino, H.Iwasaki, M.Kataoka, M.Ariyoshi, T.Fujita, H.Shinagawa, K.Morikawa.
 
  ABSTRACT  
 
In prokaryotes, RuvA-RuvB complexes play a crucial role in the migration of the Holliday junction, which is a key intermediate of homologous recombination. RuvA binds to the Holliday junction and enhances the ATPase activity of RuvB required for branch migration. RuvA adopts a unique domain structure, which assembles into a tetrameric molecule. The previous mutational and proteolytic analyses suggested that mutations in a carboxyl-terminal domain (domain III) impair binding of RuvA to RuvB. In order to clarify the functional role of each domain in vitro, we established the recombinant expression systems, which allow us to analyze structural and biochemical properties of each domain separately. A small-angle X-ray scattering solution study, combined with X-ray crystallographic analyses, was applied to the tetrameric full-length RuvA and its tetrameric NH2 region (domains I and II) lacking the domain III. These results demonstrated that domain III can be completely separate from the tetrameric major core of the NH2 region and freely mobile in solution, through a remarkably flexible loop. Biochemical analyses indicated that domain III not only interacts with RuvB, but also modulates its ATPase activity. This modulation may facilitate the dynamic coupling between RuvA and RuvB during branch migration.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Superposition of the full-length RuvA (white) and the NH2 region crystal structures (yellow). The worm models were generated by GRASP [Nicholls 1993]. 		Figure 8.
Figure 8. Functional model of RuvA, RuvB, and Holliday junction complex. The NH2 region, which binds Holliday junction, is represented by four ovals. Domain III, represented by a circle, is tethered to the NH2 region through a flexible loop. The RuvB ring, encircling DNA, interacts with domain III to modulate ATPase activity during branch migration.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 298, 407-416) copyright 2000.  
  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
19159486 T.Oyama, H.Oka, K.Mayanagi, T.Shirai, K.Matoba, R.Fujikane, Y.Ishino, and K.Morikawa (2009).
Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm.
  BMC Struct Biol, 9, 2.
PDB codes: 2zj2 2zj5 2zj8 2zja
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.  
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.  
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.  
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.  
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.  
11171970 K.Yamada, N.Kunishima, K.Mayanagi, T.Ohnishi, T.Nishino, H.Iwasaki, H.Shinagawa, and K.Morikawa (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.
PDB code: 1hqc
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
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.