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PDBsum entry 1ph6
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protein dna_rna metals Protein-protein interface(s) links
DNA binding protein/DNA PDB id
1ph6

 

 

 

 

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Contents
Protein chains
452 a.a. *
217 a.a. *
DNA/RNA
Metals
_NA ×5
Waters ×303
* Residue conservation analysis
PDB id:
1ph6
Name: DNA binding protein/DNA
Title: Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssdna ggggttttgtgg
Structure: 5'-d( Gp Gp Gp Gp Tp Tp Tp Tp Gp Gp Gp Gp T)-3'. Chain: g, h. Engineered: yes. Other_details: chains g and h are a g-quartet linked DNA dimer, 3' terminal single strand DNA sequence of macronuclear telomeres.. 5'-d( Gp Gp Gp Gp Tp Tp Tp Tp Gp Tp Gp G)-3'. Chain: d. Engineered: yes. Other_details: chain d is single strand DNA, 3' terminal single
Source: Synthetic: yes. Other_details: synthesized. Sterkiella nova. Organism_taxid: 200597. Gene: mac-56a and mac-56k and mac-56s. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: mac-41a and mac-41s.
Biol. unit: Pentamer (from PQS)
Resolution:
2.10Å     R-factor:   0.242     R-free:   0.276
Authors: D.L.Theobald,S.C.Schultz
Key ref: D.L.Theobald and S.C.Schultz (2003). Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes. Embo J, 22, 4314-4324. PubMed id: 12912928
Date:
29-May-03     Release date:   17-Jun-03    
PROCHECK
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 Headers
 References

Protein chain
P29549  (TEBA_STENO) -  Telomere-binding protein subunit alpha from Sterkiella nova
Seq:
Struc: 		495 a.a.
452 a.a.
Protein chain
P16458  (TEBB_STENO) -  Telomere-binding protein subunit beta from Sterkiella nova
Seq:
Struc: 		385 a.a.
217 a.a.
Key:    Secondary structure  CATH domain

DNA/RNA chains
  G-G-G-G-T-T-T-T-G-G-G-G 12 bases
  G-G-G-T-T-T-T-G-T-G-G 11 bases
  G-G-G-G-T-T-T-T-G-G-G-G 12 bases

 

 
Embo J 22:4314-4324 (2003)
PubMed id: 12912928  
 
 
Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes.
D.L.Theobald, S.C.Schultz.
 
  ABSTRACT  
 
Sequence-specific protein recognition of single-stranded nucleic acids is critical for many fundamental cellular processes, such as DNA replication, DNA repair, transcription, translation, recombination, apoptosis and telomere maintenance. To explore the mechanisms of sequence-specific ssDNA recognition, we determined the crystal structures of 10 different non-cognate ssDNAs complexed with the Oxytricha nova telomere end-binding protein (OnTEBP) and evaluated their corresponding binding affinities (PDB ID codes 1PH1-1PH9 and 1PHJ). The thermodynamic and structural effects of these sequence perturbations could not have been predicted based solely upon the cognate structure. OnTEBP accommodates non-cognate nucleotides by both subtle adjustments and surprisingly large structural rearrangements in the ssDNA. In two complexes containing ssDNA intermediates that occur during telomere extension by telomerase, entire nucleotides are expelled from the complex. Concurrently, the sequence register of the ssDNA shifts to re-establish a more cognate-like pattern. This phenomenon, termed nucleotide shuffling, may be of general importance in protein recognition of single-stranded nucleic acids. This set of structural and thermodynamic data highlights a fundamental difference between protein recognition of ssDNA versus dsDNA.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21397192 J.C.Liao, R.Lam, V.Brazda, S.Duan, M.Ravichandran, J.Ma, T.Xiao, W.Tempel, X.Zuo, Y.X.Wang, N.Y.Chirgadze, and C.H.Arrowsmith (2011).
Interferon-inducible protein 16: insight into the interaction with tumor suppressor p53.
  Structure, 19, 418-429.  
20172959 S.Zhang, B.Liu, H.Yang, Y.Tian, G.Liu, L.Li, and H.Tan (2010).
Characterization of EndoTT, a novel single-stranded DNA-specific endonuclease from Thermoanaerobacter tengcongensis.
  Nucleic Acids Res, 38, 3709-3720.  
19783822 E.V.Shakirov, X.Song, J.A.Joseph, and D.E.Shippen (2009).
POT1 proteins in green algae and land plants: DNA-binding properties and evidence of co-evolution with telomeric DNA.
  Nucleic Acids Res, 37, 7455-7467.  
19518131 J.E.Croy, S.E.Altschuler, N.E.Grimm, and D.S.Wuttke (2009).
Nonadditivity in the recognition of single-stranded DNA by the schizosaccharomyces pombe protection of telomeres 1 DNA-binding domain, Pot1-DBD.
  Biochemistry, 48, 6864-6875.  
18477633 D.Svozil, J.Kalina, M.Omelka, and B.Schneider (2008).
DNA conformations and their sequence preferences.
  Nucleic Acids Res, 36, 3690-3706.  
18611948 K.Hekman, K.Guja, C.Larkin, and J.F.Schildbach (2008).
An intrastrand three-DNA-base interaction is a key specificity determinant of F transfer initiation and of F TraI relaxase DNA recognition and cleavage.
  Nucleic Acids Res, 36, 4565-4572.  
17252586 M.J.Bobeck, and G.D.Glick (2007).
Role of conformational dynamics in sequence-specific autoantibody*ssDNA recognition.
  Biopolymers, 85, 481-489.  
16890443 J.E.Croy, and D.S.Wuttke (2006).
Themes in ssDNA recognition by telomere-end protection proteins.
  Trends Biochem Sci, 31, 516-525.  
17082188 P.Buczek, and M.P.Horvath (2006).
Structural reorganization and the cooperative binding of single-stranded telomere DNA in Sterkiella nova.
  J Biol Chem, 281, 40124-40134.
PDB code: 2i0q
15632080 C.Kelleher, I.Kurth, and J.Lingner (2005).
Human protection of telomeres 1 (POT1) is a negative regulator of telomerase activity in vitro.
  Mol Cell Biol, 25, 808-818.  
15306852 A.A.Thompson, and O.B.Peersen (2004).
Structural basis for proteolysis-dependent activation of the poliovirus RNA-dependent RNA polymerase.
  EMBO J, 23, 3462-3471.
PDB codes: 1ra6 1ra7 1raj 1tql
14966288 C.Wei, and C.M.Price (2004).
Cell cycle localization, dimerization, and binding domain architecture of the telomere protein cPot1.
  Mol Cell Biol, 24, 2091-2102.  
12962623 D.L.Theobald, R.B.Cervantes, V.Lundblad, and D.S.Wuttke (2003).
Homology among telomeric end-protection proteins.
  Structure, 11, 1049-1050.  
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.

 

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