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PDBsum entry 1ftt

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protein links
DNA binding protein PDB id
1ftt
Jmol
Contents
Protein chain
68 a.a. *
* Residue conservation analysis
PDB id:
1ftt
Name: DNA binding protein
Title: Thyroid transcription factor 1 homeodomain (rattus norvegicus)
Structure: Thyroid transcription factor 1 homeodomain. Chain: a. Synonym: ttf-1 hd. Engineered: yes. Other_details: ph = 4.0 - 4.1, t = 287 - 289 k, nan3 (w/v) = 0.2 - 0.5%
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: rat ttf-1. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
NMR struc: 20 models
Authors: F.Fogolari,G.Esposito,G.Damante,S.Formisano,R.Di Lauro, P.Viglino
Key ref: G.Esposito et al. (1996). Analysis of the solution structure of the homeodomain of rat thyroid transcription factor 1 by 1H-NMR spectroscopy and restrained molecular mechanics. Eur J Biochem, 241, 101-113. PubMed id: 8898894
Date:
03-Oct-95     Release date:   29-Jan-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P23441  (NKX21_RAT) -  Homeobox protein Nkx-2.1
Seq:
Struc:
372 a.a.
68 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     DNA binding     2 terms  

 

 
Eur J Biochem 241:101-113 (1996)
PubMed id: 8898894  
 
 
Analysis of the solution structure of the homeodomain of rat thyroid transcription factor 1 by 1H-NMR spectroscopy and restrained molecular mechanics.
G.Esposito, F.Fogolari, G.Damante, S.Formisano, G.Tell, A.Leonardi, R.Di Lauro, P.Viglino.
 
  ABSTRACT  
 
The solution structure of the rat thyroid transcription factor 1 (TTF-1) homeodomain has been elucidated by 1H-NMR and restrained modeling. The TTF-1 homeodomain folds in the same manner as classical homeodomains, with three helices, a loose loop between the first two helices, and a tight turn between helix II and helix III. The typical assembly of the hydrophobic core is maintained and N-capping motifs are identified in helix I and helix III. The N-terminal stretch of helix II exhibits some mobility, similar to the preceding loop region, which may be related to its anomalous capping. The N-terminal decapeptide and the C-terminal octapeptide of the molecule (68 residues long) are disordered. All the previous characteristics are shared by all known isolated homeodomain structures. An important difference among these structures occurs at the C-terminal extension of helix III, which is either disordered or helically folded. In the TTF-1 homeodomain, the C-terminal extension of helix III (residues 51-59) appears structured, albeit not as rigidly as the preceding portion. Analysis of the NOEs and hydrogendeuterium exchange of backbone amides provides evidence for discontinuity between the two moieties of helix III, which is introduced by a tightening or a kink of residues 51-53.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19336474 A.Carré, G.Szinnai, M.Castanet, S.Sura-Trueba, E.Tron, I.Broutin-L'Hermite, P.Barat, C.Goizet, D.Lacombe, M.L.Moutard, C.Raybaud, C.Raynaud-Ravni, S.Romana, H.Ythier, J.Léger, and M.Polak (2009).
Five new TTF1/NKX2.1 mutations in brain-lung-thyroid syndrome: rescue by PAX8 synergism in one case.
  Hum Mol Genet, 18, 2266-2276.  
  18997347 C.Genis, P.Scone, H.Kasahara, and H.J.Nam (2008).
Crystallization and preliminary X-ray analysis of the NKX2.5 homeodomain in complex with DNA.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1079-1082.  
18167145 D.Gümral, L.Nadalin, A.Corazza, F.Fogolari, G.Damante, P.Viglino, and G.Esposito (2008).
Helix mobility and recognition function of the rat thyroid transcription factor 1 homeodomain - hints from 15N-NMR relaxation studies.
  FEBS J, 275, 435-448.  
17729273 P.Del Vecchio, P.Carullo, G.Barone, B.Pagano, G.Graziano, A.Iannetti, R.Acquaviva, A.Leonardi, and S.Formisano (2008).
Conformational stability and DNA binding energetics of the rat thyroid transcription factor 1 homeodomain.
  Proteins, 70, 748-760.  
16287076 A.Corazza, C.Rosano, K.Pagano, V.Alverdi, G.Esposito, C.Capanni, F.Bemporad, G.Plakoutsi, M.Stefani, F.Chiti, S.Zuccotti, M.Bolognesi, and P.Viglino (2006).
Structure, conformational stability, and enzymatic properties of acylphosphatase from the hyperthermophile Sulfolobus solfataricus.
  Proteins, 62, 64-79.
PDB codes: 1y9o 2bjd 2bje
16493447 A.V.D'Elia, C.Puppin, L.Pellizzari, A.Pianta, E.Bregant, R.Lonigro, G.Tell, F.Fogolari, V.van Heyningen, and G.Damante (2006).
Molecular analysis of a human PAX6 homeobox mutant.
  Eur J Hum Genet, 14, 744-751.  
15143176 J.E.Ploski, M.K.Shamsher, and A.Radu (2004).
Paired-type homeodomain transcription factors are imported into the nucleus by karyopherin 13.
  Mol Cell Biol, 24, 4824-4834.  
12923178 E.J.Stollar, U.Mayor, S.C.Lovell, L.Federici, S.M.Freund, A.R.Fersht, and B.F.Luisi (2003).
Crystal structures of engrailed homeodomain mutants: implications for stability and dynamics.
  J Biol Chem, 278, 43699-43708.
PDB codes: 1p7i 1p7j
11847272 G.Verdone, A.Corazza, P.Viglino, F.Pettirossi, S.Giorgetti, P.Mangione, A.Andreola, M.Stoppini, V.Bellotti, and G.Esposito (2002).
The solution structure of human beta2-microglobulin reveals the prodromes of its amyloid transition.
  Protein Sci, 11, 487-499.
PDB code: 1jnj
11668629 A.V.D'Elia, G.Tell, I.Paron, L.Pellizzari, R.Lonigro, and G.Damante (2001).
Missense mutations of human homeoboxes: A review.
  Hum Mutat, 18, 361-374.  
10933814 T.Sprules, N.Green, M.Featherstone, and K.Gehring (2000).
Conformational changes in the PBX homeodomain and C-terminal extension upon binding DNA and HOX-derived YPWM peptides.
  Biochemistry, 39, 9943-9950.
PDB code: 1du6
10605826 G.Tell, R.Acquaviva, S.Formisano, F.Fogolari, C.Pucillo, and G.Damante (1999).
Comparative stability analysis of the thyroid transcription factor 1 and Antennapedia homeodomains: evidence for residue 54 in controlling the structural stability of the recognition helix.
  Int J Biochem Cell Biol, 31, 1339-1353.  
9565750 J.P.Schneider, A.Lombardi, and W.F.DeGrado (1998).
Analysis and design of three-stranded coiled coils and three-helix bundles.
  Fold Des, 3, R29-R40.  
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.