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PDBsum entry 1p7i

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protein ligands Protein-protein interface(s) links
DNA binding protein PDB id
1p7i
Jmol
Contents
Protein chains
53 a.a. *
50 a.a. *
50 a.a. *
56 a.a. *
Ligands
NHE
Waters ×100
* Residue conservation analysis
PDB id:
1p7i
Name: DNA binding protein
Title: Crystal structure of engrailed homeodomain mutant k52a
Structure: Segmentation polarity homeobox protein engrailed. Chain: a, b, c, d. Fragment: homeodomain. Engineered: yes. Mutation: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: en. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.10Å     R-factor:   0.202     R-free:   0.240
Authors: E.J.Stollar,U.Mayor,S.C.Lovell,L.Federici,S.M.Freund,A.R.Fer B.F.Luisi
Key ref:
E.J.Stollar et al. (2003). Crystal structures of engrailed homeodomain mutants: implications for stability and dynamics. J Biol Chem, 278, 43699-43708. PubMed id: 12923178 DOI: 10.1074/jbc.M308029200
Date:
02-May-03     Release date:   14-Oct-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02836  (HMEN_DROME) -  Segmentation polarity homeobox protein engrailed
Seq:
Struc:
 
Seq:
Struc:
552 a.a.
53 a.a.*
Protein chain
Pfam   ArchSchema ?
P02836  (HMEN_DROME) -  Segmentation polarity homeobox protein engrailed
Seq:
Struc:
 
Seq:
Struc:
552 a.a.
50 a.a.*
Protein chain
Pfam   ArchSchema ?
P02836  (HMEN_DROME) -  Segmentation polarity homeobox protein engrailed
Seq:
Struc:
 
Seq:
Struc:
552 a.a.
50 a.a.*
Protein chain
Pfam   ArchSchema ?
P02836  (HMEN_DROME) -  Segmentation polarity homeobox protein engrailed
Seq:
Struc:
 
Seq:
Struc:
552 a.a.
56 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 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     transcription regulatory region sequence-specific DNA binding     4 terms  

 

 
DOI no: 10.1074/jbc.M308029200 J Biol Chem 278:43699-43708 (2003)
PubMed id: 12923178  
 
 
Crystal structures of engrailed homeodomain mutants: implications for stability and dynamics.
E.J.Stollar, U.Mayor, S.C.Lovell, L.Federici, S.M.Freund, A.R.Fersht, B.F.Luisi.
 
  ABSTRACT  
 
We report the crystal structures and biophysical characterization of two stabilized mutants of the Drosophila Engrailed homeodomain that have been engineered to minimize electrostatic repulsion. Four independent copies of each mutant occupy the crystal lattice, and comparison of these structures illustrates variation that can be partly ascribed to networks of correlated conformational adjustments. Central to one network is leucine 26 (Leu26), which occupies alternatively two side chain rotameric conformations (-gauche and trans) and different positions within the hydrophobic core. Similar sets of conformational substates are observed in other Engrailed structures and in another homeodomain. The pattern of structural adjustments can account for NMR relaxation data and sequence co-variation networks in the wider homeodomain family. It may also explain the dysfunction associated with a P26L mutation in the human ARX homeodomain protein. Finally, we observe a novel dipolar interaction between a conserved tryptophan and a water molecule positioned along the normal to the indole ring. This interaction may explain the distinctive fluorescent properties of the homeodomain family.
 
  Selected figure(s)  
 
Figure 2.
FIG. 2. Structure and electrostatic surfaces of En-HD and its mutants. A, schematic illustration of the homeodomain fold as represented by copy A of the mutant K52E. The side chains of residues 17, 48, 52, and 55 are shown. B, electrostatic surface of wild type, K52E copy A (C), and K52A copy A (D). The view is from the same perspective as shown in A. For clarity and for purposes of comparison (because of poor density in some cases), the side chains of residues Arg24 and Arg29 were not included and the N terminus begins at residue 7. E, cartoon depiction of the site of mutation for the K52E mutant, and F, the K52A mutant. Each copy is color coded, copy A (blue), copy B (red), copy C (yellow), and copy D (pink). The dashed lines indicate salt bridge links.
Figure 5.
FIG. 5. Leu26 network. A, the Leu26 network in K52E and wild type. Each copy is color coded, blue is copy A, red is copy B, yellow is copy C, pink is copy D, and green is wild type (as in Fig. 2). The backbone atoms for residues 23-25 are also shown. B, the Leu26 network in MATa1 homeodomain. Blue is from Protein data bank entry 1MH3 [PDB] and red is from 1MH4 [PDB] . C, copy B (green) from the wild type En-HD·DNA complex (3HDD [PDB] ) superimposed onto the mutant En-HD K52E. D, copy A (green) from the mutant Q50A En-HD·DNA complex (1DUO [PDB] ) superimposed onto the mutant En-HD K52E.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 43699-43708) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20944750 A.M.Ruschak, T.L.Religa, S.Breuer, S.Witt, and L.E.Kay (2010).
The proteasome antechamber maintains substrates in an unfolded state.
  Nature, 467, 868-871.  
19561080 M.Torrado, J.Revuelta, C.Gonzalez, F.Corzana, A.Bastida, and J.L.Asensio (2009).
Role of conserved salt bridges in homeodomain stability and DNA binding.
  J Biol Chem, 284, 23765-23779.  
18394579 F.Alasti, A.Sadeghi, M.H.Sanati, M.Farhadi, E.Stollar, T.Somers, and G.Van Camp (2008).
A mutation in HOXA2 is responsible for autosomal-recessive microtia in an Iranian family.
  Am J Hum Genet, 82, 982-991.  
18274703 T.L.Religa (2008).
Comparison of multiple crystal structures with NMR data for engrailed homeodomain.
  J Biomol NMR, 40, 189-202.
PDB code: 2jwt
17517666 T.L.Religa, C.M.Johnson, D.M.Vu, S.H.Brewer, R.B.Dyer, and A.R.Fersht (2007).
The helix-turn-helix motif as an ultrafast independently folding domain: the pathway of folding of Engrailed homeodomain.
  Proc Natl Acad Sci U S A, 104, 9272-9277.
PDB code: 2p81
17095606 I.A.Hubner, E.J.Deeds, and E.I.Shakhnovich (2006).
Understanding ensemble protein folding at atomic detail.
  Proc Natl Acad Sci U S A, 103, 17747-17752.  
16943445 S.Lim, and S.J.Franklin (2006).
Engineered lanthanide-binding metallohomeodomains: designing folded chimeras by modular turn substitution.
  Protein Sci, 15, 2159-2165.  
16292553 S.W.Wong-Deyrup, Y.Kim, and S.J.Franklin (2006).
Sequence preference in DNA binding: de novo designed helix-turn-helix metallopeptides recognize a family of DNA target sites.
  J Biol Inorg Chem, 11, 17-25.  
15326588 E.J.Stollar, J.L.Gelpí, S.Velankar, A.Golovin, M.Orozco, and B.F.Luisi (2004).
Unconventional interactions between water and heterocyclic nitrogens in protein structures.
  Proteins, 57, 1-8.  
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.