1KFT | pdb_00001kft

Solution Structure of the C-Terminal domain of UvrC from E-coli

• PDB DOI: https://doi.org/10.2210/pdb1KFT/pdb
• BMRB: 5217

• Classification: DNA BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-11-23 Released: 2002-11-20 
• Deposition Author(s): Singh, S., Folkers, G.E., Bonvin, A.M.J.J., Boelens, R., Wechselberger, R., Niztayev, A., Kaptein, R.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 22 
• Selection Criteria: no NOE distance violations > 0.5A and lowest energies after refining the best 50 of the initial 200 in explicit water 

Literature

Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli

Singh, S., Folkers, G.E., Bonvin, A.M.J.J., Boelens, R., Wechselberger, R., Niztayev, A., Kaptein, R.

(2002) EMBO J 21: 6257-6266

• PubMed: 12426397 
• DOI: https://doi.org/10.1093/emboj/cdf627
• Primary Citation Related Structures: 
  1KFT


• PubMed 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.

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Organizational Affiliation: 
• Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.58 kDa 
• Atom Count: 432 
• Modeled Residue Count: 56 
• Deposited Residue Count: 78 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Excinuclease ABC subunit C	A	78	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A8G0 (Escherichia coli (strain K12)) Explore P0A8G0  Go to UniProtKB:  P0A8G0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 22 
• Selection Criteria: no NOE distance violations > 0.5A and lowest energies after refining the best 50 of the initial 200 in explicit water 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-20 
Deposition Author(s): Singh, S., Folkers, G.E., Bonvin, A.M.J.J., Boelens, R., Wechselberger, R., Niztayev, A., Kaptein, R.

Revision History  

• Version 1.0: 2002-11-20
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-05-29
  Changes: Data collection