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DNA binding protein PDB id
1kft
Jmol
Contents
Protein chain
56 a.a. *
* Residue conservation analysis
PDB id:
1kft
Name: DNA binding protein
Title: Solution structure of thE C-terminal domain of uvrc from e- coli
Structure: Excinuclease abc subunit c. Chain: a. Fragment: hhh domain(c-terminal domain). Synonym: uvrc. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: de3. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 22 models
Authors: S.Singh,G.E.Folkers,A.M.J.J.Bonvin,R.Boelens, R.Wechselberger,A.Niztayev,R.Kaptein
Key ref:
S.Singh et al. (2002). Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli. EMBO J, 21, 6257-6266. PubMed id: 12426397 DOI: 10.1093/emboj/cdf627
Date:
23-Nov-01     Release date:   20-Nov-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A8G2  (UVRC_ECO57) -  UvrABC system protein C
Seq:
Struc:
 
Seq:
Struc:
610 a.a.
56 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA repair   1 term 
  Biochemical function     DNA binding     1 term  

 

 
DOI no: 10.1093/emboj/cdf627 EMBO J 21:6257-6266 (2002)
PubMed id: 12426397  
 
 
Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli.
S.Singh, G.E.Folkers, A.M.Bonvin, R.Boelens, R.Wechselberger, A.Niztayev, R.Kaptein.
 
  ABSTRACT  
 
The C-terminal domain of the UvrC protein (UvrC CTD) is essential for 5' incision in the prokaryotic nucleotide excision repair process. We have determined the three-dimensional structure of the UvrC CTD using heteronuclear NMR techniques. The structure shows two helix-hairpin-helix (HhH) motifs connected by a small connector helix. The UvrC CTD is shown to mediate structure-specific DNA binding. The domain binds to a single-stranded-double-stranded junction DNA, with a strong specificity towards looped duplex DNA that contains at least six unpaired bases per loop ("bubble DNA"). Using chemical shift perturbation experiments, the DNA-binding surface is mapped to the first hairpin region encompassing the conserved glycine-valine-glycine residues followed by lysine-arginine-arginine, a positively charged surface patch and the second hairpin region consisting of glycine-isoleucine-serine. A model for the protein-DNA complex is proposed that accounts for this specificity.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 The NMR solution structure of the UvrC CTD. (A) Backbone stereo view (residues 28−78) of the NMR ensemble (22 structures); the hairpins are coloured in blue. (B) Ribbon view of a representative UvrC CTD structure (closest to average) for residues 23−78. h1 and h2 are the hairpins of HhH motifs. The structures were displayed using the molecular graphics program MOLMOL (Koradi et al., 1996).
Figure 7.
Figure 7 Model representing the interaction of the UvrC CTD with the ds−ss junction. Glycines are coloured red, lysine in blue and threonine in green. This model was obtained by superimposing the two hairpins of UvrC CTD on to the corresponding loops of RNA polymerase II (domain containing the active site of the Rpb1 subunit, PDB accession No. 16IH, see Materials and methods). The structure was generated using the software VMD (Humphrey et al., 1996).
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 6257-6266) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20008103 R.D.Hutton, T.D.Craggs, M.F.White, and J.C.Penedo (2010).
PCNA and XPF cooperate to distort DNA substrates.
  Nucleic Acids Res, 38, 1664-1675.  
18518821 A.Ciccia, N.McDonald, and S.C.West (2008).
Structural and functional relationships of the XPF/MUS81 family of proteins.
  Annu Rev Biochem, 77, 259-287.  
17912758 D.Das, K.Tripsianes, N.G.Jaspers, J.H.Hoeijmakers, R.Kaptein, R.Boelens, and G.E.Folkers (2008).
The HhH domain of the human DNA repair protein XPF forms stable homodimers.
  Proteins, 70, 1551-1563.
PDB code: 2aq0
18343204 D.L.Croteau, Y.Peng, and B.Van Houten (2008).
DNA repair gets physical: mapping an XPA-binding site on ERCC1.
  DNA Repair (Amst), 7, 819-826.  
18158267 D.Pakotiprapha, Y.Inuzuka, B.R.Bowman, G.F.Moolenaar, N.Goosen, D.Jeruzalmi, and G.L.Verdine (2008).
Crystal structure of Bacillus stearothermophilus UvrA provides insight into ATP-modulated dimerization, UvrB interaction, and DNA binding.
  Mol Cell, 29, 122-133.
PDB code: 2r6f
18539732 P.Lagerbäck, and K.Carlson (2008).
Amino acid residues in the GIY-YIG endonuclease II of phage T4 affecting sequence recognition and binding as well as catalysis.
  J Bacteriol, 190, 5533-5544.  
18184592 R.N.de Jong, V.Truffault, T.Diercks, E.Ab, M.A.Daniels, R.Kaptein, and G.E.Folkers (2008).
Structure and DNA binding of the human Rtf1 Plus3 domain.
  Structure, 16, 149-159.
PDB code: 2bze
17245438 E.Karakas, J.J.Truglio, D.Croteau, B.Rhau, L.Wang, B.Van Houten, and C.Kisker (2007).
Structure of the C-terminal half of UvrC reveals an RNase H endonuclease domain with an Argonaute-like catalytic triad.
  EMBO J, 26, 613-622.
PDB codes: 2nrr 2nrt 2nrv 2nrw 2nrx 2nrz
17720715 K.Tripsianes, G.E.Folkers, C.Zheng, D.Das, J.S.Grinstead, R.Kaptein, and R.Boelens (2007).
Analysis of the XPA and ssDNA-binding surfaces on the central domain of human ERCC1 reveals evidence for subfunctionalization.
  Nucleic Acids Res, 35, 5789-5798.
PDB code: 2jpd
16646971 S.Dunin-Horkawicz, M.Feder, and J.M.Bujnicki (2006).
Phylogenomic analysis of the GIY-YIG nuclease superfamily.
  BMC Genomics, 7, 98.  
15654870 A.D.van Dijk, R.Boelens, and A.M.Bonvin (2005).
Data-driven docking for the study of biomolecular complexes.
  FEBS J, 272, 293-312.  
16132081 E.P.Rocha, E.Cornet, and B.Michel (2005).
Comparative and evolutionary analysis of the bacterial homologous recombination systems.
  PLoS Genet, 1, e15.  
16338413 K.Tripsianes, G.Folkers, E.Ab, D.Das, H.Odijk, N.G.Jaspers, J.H.Hoeijmakers, R.Kaptein, and R.Boelens (2005).
The structure of the human ERCC1/XPF interaction domains reveals a complementary role for the two proteins in nucleotide excision repair.
  Structure, 13, 1849-1858.
PDB code: 1z00
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
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
15932882 Y.J.Choi, K.S.Ryu, Y.M.Ko, Y.K.Chae, J.G.Pelton, D.E.Wemmer, and B.S.Choi (2005).
Biophysical characterization of the interaction domains and mapping of the contact residues in the XPF-ERCC1 complex.
  J Biol Chem, 280, 28644-28652.  
15333947 J.Lally, M.Newman, J.Murray-Rust, A.Fadden, Y.Kawarabayasi, and N.McDonald (2004).
Crystallization of the xeroderma pigmentosum group F endonuclease from Aeropyrum pernix.
  Acta Crystallogr D Biol Crystallogr, 60, 1658-1661.  
15165242 K.Carlson, P.Lagerbäck, and A.C.Nyström (2004).
Bacteriophage T4 endonuclease II: concerted single-strand nicks yield double-strand cleavage.
  Mol Microbiol, 52, 1403-1411.  
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.