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PDBsum entry 2i13

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protein dna_rna ligands metals Protein-protein interface(s) links
DNA binding protein/DNA PDB id
2i13
Jmol
Contents
Protein chains
151 a.a. *
DNA/RNA
Ligands
GOL ×4
Metals
_ZN ×11
Waters ×417
* Residue conservation analysis
PDB id:
2i13
Name: DNA binding protein/DNA
Title: Aart, a six finger zinc finger designed to recognize ann tri
Structure: 5'-d( Cp Ap Gp Ap Tp Gp Tp Ap Gp Gp Gp Ap Ap Ap A Cp Gp Gp G)-3'. Chain: c, e. Engineered: yes. 5'-d( Gp Cp Cp Cp Gp Gp Gp Cp Tp Tp Tp Tp Cp Cp C Ap Tp Cp T)-3'. Chain: d, f. Engineered: yes. Aart.
Source: Synthetic: yes. Other_details: solid phase synthesis by phosphoramidite che mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
Resolution:
1.96Å     R-factor:   0.203     R-free:   0.249
Authors: N.C.Horton,D.J.Segal,M.Bhakta,J.W.Crotty,C.F.Barbas Iii
Key ref:
D.J.Segal et al. (2006). Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA. J Mol Biol, 363, 405-421. PubMed id: 16963084 DOI: 10.1016/j.jmb.2006.08.016
Date:
12-Aug-06     Release date:   03-Oct-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q07230  (ZSCA2_MOUSE) -  Zinc finger and SCAN domain-containing protein 2
Seq:
Struc:
 
Seq:
Struc:
614 a.a.
151 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 47 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleic acid binding     2 terms  

 

 
DOI no: 10.1016/j.jmb.2006.08.016 J Mol Biol 363:405-421 (2006)
PubMed id: 16963084  
 
 
Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA.
D.J.Segal, J.W.Crotty, M.S.Bhakta, C.F.Barbas, N.C.Horton.
 
  ABSTRACT  
 
Cys2-His2 zinc fingers are one of the most common types of DNA-binding domains. Modifications to zinc-finger binding specificity have recently enabled custom DNA-binding proteins to be designed to a wide array of target sequences. We present here a 1.96 A structure of Aart, a designed six-zinc finger protein, bound to a consensus DNA target site. This is the first structure of a designed protein with six fingers, and was intended to provide insights into the unusual affinity and specificity characteristics of this protein. Most protein-DNA contacts were found to be consistent with expectations, while others were unanticipated or insufficient to explain specificity. Several were unexpectedly mediated by glycerol, water molecules or amino acid-base stacking interactions. These results challenge some conventional concepts of recognition, particularly the finding that triplets containing 5'A, C, or T are typically not specified by direct interaction with the amino acid in position 6 of the recognition helix.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Protein and DNA sequences used in this study. (a) Aart sequence. Recognition helix residues of each zinc finger shown in bold. (b) Sequence of DNA duplex cocrystallized with Aart. X indicates 5-bromouracil in the brominated DNA, and thymine in the native DNA. The structure of Aart with non-brominated DNA was used in all structural analyses.
Figure 5.
Figure 5. Stereo Figures of Aart/DNA interactions. Colored by atom type (green, carbon; blue, nitrogen; red, oxygen). Spheres show the position of methyl groups. Water molecules are shown as small red spheres. Hydrogen bonds between the protein and DNA are shown as dotted lines. (a) Finger 1 of molecule A. (b) Finger 2 of molecule A. (c) Finger 3 of molecule A. Gol1, glycerol.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 363, 405-421) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20360772 B.Gonzalez, L.J.Schwimmer, R.P.Fuller, Y.Ye, L.Asawapornmongkol, and C.F.Barbas (2010).
Modular system for the construction of zinc-finger libraries and proteins.
  Nat Protoc, 5, 791-810.  
20565873 C.C.Chou, M.Rajasekaran, and C.Chen (2010).
An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking.
  BMC Bioinformatics, 11, 334.  
20197039 D.Jantz, and J.M.Berg (2010).
Probing the DNA-binding affinity and specificity of designed zinc finger proteins.
  Biophys J, 98, 852-860.  
20717154 F.D.Urnov, E.J.Rebar, M.C.Holmes, H.S.Zhang, and P.D.Gregory (2010).
Genome editing with engineered zinc finger nucleases.
  Nat Rev Genet, 11, 636-646.  
19965883 N.A.Temiz, A.Trapp, O.A.Prokopyev, and C.J.Camacho (2010).
Optimization of minimum set of protein-DNA interactions: a quasi exact solution with minimum over-fitting.
  Bioinformatics, 26, 319-325.  
19843614 A.Zykovich, I.Korf, and D.J.Segal (2009).
Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing.
  Nucleic Acids Res, 37, e151.  
19056825 J.D.Sander, P.Zaback, J.K.Joung, D.F.Voytas, and D.Dobbs (2009).
An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins.
  Nucleic Acids Res, 37, 506-515.  
19429892 N.A.Temiz, and C.J.Camacho (2009).
Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface.
  Nucleic Acids Res, 37, 4076-4088.  
19282480 R.M.Gordley, C.A.Gersbach, and C.F.Barbas (2009).
Synthesis of programmable integrases.
  Proc Natl Acad Sci U S A, 106, 5053-5058.  
19701937 S.Sakkhachornphop, S.Jiranusornkul, K.Kodchakorn, S.Nangola, T.Sirisanthana, and C.Tayapiwatana (2009).
Designed zinc finger protein interacting with the HIV-1 integrase recognition sequence at 2-LTR-circle junctions.
  Protein Sci, 18, 2219-2230.  
18762194 A.C.Babic, E.J.Little, V.M.Manohar, J.Bitinaite, and N.C.Horton (2008).
DNA distortion and specificity in a sequence-specific endonuclease.
  J Mol Biol, 383, 186-204.
PDB codes: 3e3y 3e40 3e41 3e42 3e43 3e44 3e45
18366021 A.Marabotti, F.Spyrakis, A.Facchiano, P.Cozzini, S.Alberti, G.E.Kellogg, and A.Mozzarelli (2008).
Energy-based prediction of amino acid-nucleotide base recognition.
  J Comput Chem, 29, 1955-1969.  
18654629 Y.Fu, M.Sinha, C.L.Peterson, and Z.Weng (2008).
The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome.
  PLoS Genet, 4, e1000138.  
17526515 J.D.Sander, P.Zaback, J.K.Joung, D.F.Voytas, and D.Dobbs (2007).
Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool.
  Nucleic Acids Res, 35, W599-W605.  
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.