PDBsum entry: 1c7y

Recombination/DNA

PDB id: 1c7y

Contents

Protein chain

199 a.a. *

DNA/RNA

* Residue conservation analysis

PDB id:

1c7y

Name:

Recombination/DNA

Title:

E.Coli ruva-holliday junction complex

Structure:

Holliday junction DNA helicase ruva. Chain: a. Engineered: yes. DNA (5'- d(p Dap Dap Dgp Dtp Dtp Dgp Dgp Dgp Dap Dtp Dtp Dgp Dt)- 3'). Chain: b. Engineered: yes. DNA (5'-

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes

Biol. unit:

Octamer (from PDB file)

Resolution:

3.10Å R-factor: 0.249 R-free: 0.279

Authors:

M.Ariyoshi,T.Nishino,H.Iwasaki,H.Shinagawa,K.Morikawa

Key ref:

M.Ariyoshi et al. (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. PubMed id: 10890893 DOI: 10.1073/pnas.140212997

Date:

03-Apr-00 Release date: 21-Jul-00

Protein chain

P0A809  (RUVA_ECOLI) -  Holliday junction ATP-dependent DNA helicase RuvA

Seq: 203 a.a.

Struc: 199 a.a.

Enzyme reactions

• Enzyme class: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H₂O = ADP + phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• 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: 10.1073/pnas.140212997

Proc Natl Acad Sci U S A 97:8257-8262 (2000)

PubMed id: 10890893

Crystal structure of the holliday junction DNA in complex with a single RuvA tetramer.

M.Ariyoshi, T.Nishino, H.Iwasaki, H.Shinagawa, K.Morikawa.

ABSTRACT

In the major pathway of homologous DNA recombination in prokaryotic cells, the Holliday junction intermediate is processed through its association with RuvA, RuvB, and RuvC proteins. Specific binding of the RuvA tetramer to the Holliday junction is required for the RuvB motor protein to be loaded onto the junction DNA, and the RuvAB complex drives the ATP-dependent branch migration. We solved the crystal structure of the Holliday junction bound to a single Escherichia coli RuvA tetramer at 3.1-A resolution. In this complex, one side of DNA is accessible for cleavage by RuvC resolvase at the junction center. The refined junction DNA structure revealed an open concave architecture with a four-fold symmetry. Each arm, with B-form DNA, in the Holliday junction is predominantly recognized in the minor groove through hydrogen bonds with two repeated helix-hairpin-helix motifs of each RuvA subunit. The local conformation near the crossover point, where two base pairs are disrupted, suggests a possible scheme for successive base pair rearrangements, which may account for smooth Holliday junction movement without segmental unwinding.

Selected figure(s)

Figure 2.
Fig. 2. Representative protein-Holliday junction interaction. (A) A DNA arm (stick representation) is recognized on the minor groove side by the two HhH motifs (green ribbon representation) of RuvA. The view of the complex is the same as that in Fig. 1B. The junction center is located at the right end of the figure. (B) Close-up view showing the interactions between RuvA and DNA. RuvA is shown in a green-colored stick representation. Hydrogen bonds formed between the protein and the DNA phosphate backbone are indicated by white dotted lines. (C) Schematic representation of protein-DNA interactions. Solid lines indicate polar interactions between the protein and DNA atoms at a distance of less than 3.2 Å. Dotted lines represent candidates for water-mediated interactions within a distance of less than 6.0 Å. (D) Ribbon representations of the single subunit of E. coli RuvA. The subunit of the free form (magenta) is superimposed onto that of the complex with the junction DNA (blue). The blue dot line indicates the structurally disordered connection between the flexible loop and domain III in the complex whereas the connection in the free form structure is not shown. The residues, involved in DNA binding through direct (Lys-84, Gly-117, Lys-119, and Arg-123) or putative indirect (Arg-54 and Leu-113) polar interactions, are indicated on the complex model by their side chains. The side chains of Glu-55 and Asp-56, which form the acidic pin, are also indicated.

Figure 4.
Fig. 4. Structure of the Holliday junction center. (A) Fo-Fc annealed omit electron density map (>2.5 ) showing a DNA moiety within the junction center. The two bases closest to the junction center, indicated by a white stick model, were omitted from the map calculation. (B) Environments around unpaired bases in the tetrameric RuvA center. Arg-54, Glu-55, and Asp-56 of each RuvA subunit, which form the acidic pin, are shown by a ball-and-stick representation. (C) Schematic drawing of the Holliday junction structure. The synthetic Holliday junction was designed to form two pairs of opposite arms with different lengths: the north and south arms of a 12-bp DNA duplex and the east and west arms of a 13-bp DNA duplex with a single base overhang at the 5' end. Two AT base pairs disrupted at the crossover are colored by magenta. The topological features of the unpaired bases may reflect a scene during branch migration, in which the base pair rearrangements are in progress and the new base pairs will be subsequently formed.

Figures were selected by the author.