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PDBsum entry 1bw5

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protein links
DNA-binding protein PDB id
1bw5
Jmol
Contents
Protein chain
66 a.a. *
* Residue conservation analysis
PDB id:
1bw5
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
Date:
29-Sep-98     Release date:   15-Jun-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P50480  (ISL2_RAT) -  Insulin gene enhancer protein ISL-2
Seq:
Struc:
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.
 
  ABSTRACT  
 
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
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.