PDBsum entry 1bw5

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protein links
DNA-binding protein PDB id
Protein chain
66 a.a. *
* Residue conservation analysis
PDB id:
Name: DNA-binding protein
Title: The nmr solution structure of the homeodomain of the rat insulin gene enhancer protein isl-1, 50 structures
Structure: Insulin gene enhancer protein isl-1. Chain: a. Synonym: isl-1hd
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Organ: pancreas
NMR struc: 50 models
Authors: J.H.Ippel,G.Larsson,G.Behravan,J.Zdunek,M.Lundqvist, J.Schleucher,P.-O.Lycksell,S.S.Wijmenga
Key ref:
H.Ippel et al. (1999). The solution structure of the homeodomain of the rat insulin-gene enhancer protein isl-1. Comparison with other homeodomains. J Mol Biol, 288, 689-703. PubMed id: 10329173 DOI: 10.1006/jmbi.1999.2718
29-Sep-98     Release date:   15-Jun-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P50480  (ISL2_RAT) -  Insulin gene enhancer protein ISL-2
360 a.a.
66 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     DNA binding     3 terms  


DOI no: 10.1006/jmbi.1999.2718 J Mol Biol 288:689-703 (1999)
PubMed id: 10329173  
The solution structure of the homeodomain of the rat insulin-gene enhancer protein isl-1. Comparison with other homeodomains.
H.Ippel, G.Larsson, G.Behravan, J.Zdunek, M.Lundqvist, J.Schleucher, P.O.Lycksell, S.Wijmenga.
Homeodomains are one of the key families of eukaryotic DNA-binding motifs and provide an important model system for DNA recognition. We have determined a high-quality nuclear magnetic resonance (NMR) structure of the DNA-binding homeodomain of the insulin gene enhancer protein Isl-1 (Isl-1-HD). It forms the first solution structure of a homeodomain from the LIM family. It contains a well-defined inner core (residues 12-55) consisting of the classical three-helix structure observed in other homeodomains. The N terminus is unstructured up to residue 8, while the C terminus gradually becomes unstructured from residue 55 onwards. Some flexibility is evident in the loop parts of the inner core. Isl-1-HD has, despite its low sequence identity (23-34 %), a structure that is strikingly similar to that of the other homeodomains with known three-dimensional structures. Detailed analysis of Isl-1-HD and the other homeodomains rationalizes the differences in their temperature stability and explains the low stability of the Isl-1-HD in the free state (tm 22-30 degrees C). Upon DNA binding, a significant stabilization occurs (tm>55 degrees C). The low stability of Isl-1-HD (and other mammalian homeodomains) suggests that in vivo Isl-1-HD recognizes its cognate DNA from its unfolded state.
  Selected figure(s)  
Figure 6.
Figure 6. Superposition of aromatic rings Tyr22, Trp50 and Phe51 of Isl-1-HD for: (a) Set 2 using only NOE restraints; (b) Set 2 using J-coupling and NOE restraints; and (c) Set 2 (using J-coupling, NOE, and chemical shift restraints).
Figure 7.
Figure 7. The core region of the solution structure of Isl-1-HD (Set 2). Highlighted are the residues important for stabilization: (a) group I, (b) group II, (c) group III, and (d) group IV. (a) The orientation of helices I to III are indi- cated by arrows.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 288, 689-703) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17342709 D.Latek, D.Ekonomiuk, and A.Kolinski (2007).
Protein structure prediction: combining de novo modeling with sparse experimental data.
  J Comput Chem, 28, 1668-1676.  
16732181 O.Drognitz, P.Michel, D.Koczan, H.Neeff, Y.Mikami, R.Obermaier, H.J.Thiesen, U.T.Hopt, and M.Loebler (2006).
Characterization of ischemia/reperfusion-induced gene expression in experimental pancreas transplantation.
  Transplantation, 81, 1428-1434.  
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
12202384 S.Kumar, and R.Nussinov (2002).
Relationship between ion pair geometries and electrostatic strengths in proteins.
  Biophys J, 83, 1595-1612.  
11391564 G.Iurcu-Mustata, D.Van Belle, R.Wintjens, M.Prévost, and M.Rooman (2001).
Role of salt bridges in homeodomains investigated by structural analyses and molecular dynamics simulations.
  Biopolymers, 59, 145-159.  
11340660 S.Kumar, and R.Nussinov (2001).
Fluctuations in ion pairs and their stabilities in proteins.
  Proteins, 43, 433-454.  
  10752620 O.V.Galzitskaya, A.K.Surin, and H.Nakamura (2000).
Optimal region of average side-chain entropy for fast protein folding.
  Protein Sci, 9, 580-586.  
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
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