PDBsum entry 1vnd

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protein links
DNA-binding protein PDB id
Protein chain
77 a.a. *
* Residue conservation analysis
PDB id:
Name: DNA-binding protein
Title: Vnd/nk-2 protein (homeodomain), nmr
Structure: Vnd/nk-2 protein. Chain: a. Fragment: homeodomain. Engineered: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Organ: fruit. Expressed in: escherichia coli. Expression_system_taxid: 562
NMR struc: 30 models
Authors: D.H.H.Tsao,J.M.Gruschus,L.-H.Wang,M.Nirenberg,J.A.Ferretti
Key ref:
D.H.Tsao et al. (1995). The three-dimensional solution structure of the NK-2 homeodomain from Drosophila. J Mol Biol, 251, 297-307. PubMed id: 7643404 DOI: 10.1006/jmbi.1995.0435
22-May-96     Release date:   08-Nov-96    
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Protein chain
Pfam   ArchSchema ?
P22808  (VND_DROME) -  Homeobox protein vnd
723 a.a.
77 a.a.*
Key:    PfamA domain  PfamB 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  


DOI no: 10.1006/jmbi.1995.0435 J Mol Biol 251:297-307 (1995)
PubMed id: 7643404  
The three-dimensional solution structure of the NK-2 homeodomain from Drosophila.
D.H.Tsao, J.M.Gruschus, L.H.Wang, M.Nirenberg, J.A.Ferretti.
We describe the NMR determination of the three-dimensional structure of a 77 amino acid residue protein, which consists of the 60 residue NK-2 homeodomain from Drosophila melanogaster and adjacent amino acid residues. The NK-2 homeodomain protein is part of a 723 amino acid residue protein which is expressed early in embryonic development in part of the central nervous system. NK-2 was characterized using both a natural abundance and a uniformly 15N enriched sample by two-dimensional and three-dimensional NMR experiments. The average root-mean-square deviation for 30 structures for residues 8 to 53 is 0.40 A for the backbone heavy-atoms and 0.72 A for the backbone and side-chain heavy-atoms. These structures were obtained from 986 NOE-derived upper and lower bound restraints. The three-dimensional structure contains three helices which consist of homeodomain amino acid residues 10 to 22, 28 to 38 and 42 to 52, as well as a turn between helix II and III, characteristic of homeodomains. Residues 53 to 60 of the DNA recognition helix are not fully ordered in the absence of DNA. In the free state this segment adopts a flexible but helix-like structure between residues 53 and 56 and is disordered from residues 57 to 60 although, as shown previously, the helix elongates by eight residues upon binding to DNA. The role of variable residues 52, 54 and 56 in determining the structure and flexibility of the recognition helix, as well as the stability of the NK-2 homeodomain as manifested by its thermal denaturation, are discussed.
  Selected figure(s)  
Figure 2.
Figure 2. Superposition of the polypeptide backbone of the 30 structures of NK-2 homeodomain protein generated with DSPACE and refined with X-PLOR. The colors are representative of the r.m.s.d. of the 30 structures, where blue indicates very well defined, green/yellow indicate intermediate and magenta indicates very well defined.
Figure 3.
Figure 3. Superposition of the polypeptide backbone for residues 8 to 53 and the well-ordered side-chains which form the hydrophobic core in NK-2. Helix I and II are in the front part of the Figure, and helix III is at the back.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1995, 251, 297-307) copyright 1995.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
16497162 I.L.Viola, and D.H.Gonzalez (2006).
Interaction of the BELL-like protein ATH1 with DNA: role of homeodomain residue 54 in specifying the different binding properties of BELL and KNOX proteins.
  Biol Chem, 387, 31-40.  
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.  
15169783 W.Sheng, H.Yan, F.M.Rausa, R.H.Costa, and X.Liao (2004).
Structure of the hepatocyte nuclear factor 6alpha and its interaction with DNA.
  J Biol Chem, 279, 33928-33936.
PDB code: 1s7e
12538894 A.Ke, and C.Wolberger (2003).
Insights into binding cooperativity of MATa1/MATalpha2 from the crystal structure of a MATa1 homeodomain-maltose binding protein chimera.
  Protein Sci, 12, 306-312.
PDB codes: 1mh3 1mh4
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
12626758 K.Koizumi, C.Lintas, M.Nirenberg, J.S.Maeng, J.H.Ju, J.W.Mack, J.M.Gruschus, W.F.Odenwald, and J.A.Ferretti (2003).
Mutations that affect the ability of the vnd/NK-2 homeoprotein to regulate gene expression: transgenic alterations and tertiary structure.
  Proc Natl Acad Sci U S A, 100, 3119-3124.  
12093803 A.E.Tron, C.W.Bertoncini, R.L.Chan, and D.H.Gonzalez (2002).
Redox regulation of plant homeodomain transcription factors.
  J Biol Chem, 277, 34800-34807.  
12232052 L.H.Wang, R.Chmelik, and M.Nirenberg (2002).
Sequence-specific DNA binding by the vnd/NK-2 homeodomain of Drosophila.
  Proc Natl Acad Sci U S A, 99, 12721-12726.  
11726696 A.E.Tron, C.W.Bertoncini, C.M.Palena, R.L.Chan, and D.H.Gonzalez (2001).
Combinatorial interactions of two amino acids with a single base pair define target site specificity in plant dimeric homeodomain proteins.
  Nucleic Acids Res, 29, 4866-4872.  
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.  
  11779807 J.Favor, H.Peters, T.Hermann, W.Schmahl, B.Chatterjee, A.Neuhäuser-Klaus, and R.Sandulache (2001).
Molecular characterization of Pax6(2Neu) through Pax6(10Neu): an extension of the Pax6 allelic series and the identification of two possible hypomorph alleles in the mouse Mus musculus.
  Genetics, 159, 1689-1700.  
10861370 G.La Penna, S.Fausti, A.Perico, and J.A.Ferretti (2000).
Smoluchowski dynamics of the vnd/NK-2 homeodomain from Drosophila melanogaster: second-order maximum correlation approximation.
  Biopolymers, 54, 89.  
10944215 H.Watada, R.G.Mirmira, J.Kalamaras, and M.S.German (2000).
Intramolecular control of transcriptional activity by the NK2-specific domain in NK-2 homeodomain proteins.
  Proc Natl Acad Sci U S A, 97, 9443-9448.  
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
9990841 G.La Penna, M.Mormino, F.Pioli, A.Perico, R.Fioravanti, J.M.Gruschus, and J.A.Ferretti (1999).
Smoluchowski dynamics of the vnd/NK-2 homeodomain from Drosophila melanogaster: first-order mode-coupling approximation.
  Biopolymers, 49, 235-254.  
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.  
9636163 B.Xiang, S.Weiler, M.Nirenberg, and J.A.Ferretti (1998).
Structural basis of an embryonically lethal single Ala --> Thr mutation in the vnd/NK-2 homeodomain.
  Proc Natl Acad Sci U S A, 95, 7412-7416.  
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.  
9556579 S.Weiler, J.M.Gruschus, D.H.Tsao, L.Yu, L.H.Wang, M.Nirenberg, and J.A.Ferretti (1998).
Site-directed mutations in the vnd/NK-2 homeodomain. Basis of variations in structure and sequence-specific DNA binding.
  J Biol Chem, 273, 10994-11000.  
8811078 D.Fabbro, G.Tell, A.Leonardi, L.Pellizzari, C.Pucillo, R.Lonigro, S.Formisano, and G.Damante (1996).
In the TTF-1 homeodomain the contribution of several amino acids to DNA recognition depends on the bound sequence.
  Nucleic Acids Res, 24, 3283-3288.  
  8890172 G.Damante, L.Pellizzari, G.Esposito, F.Fogolari, P.Viglino, D.Fabbro, G.Tell, S.Formisano, and R.Di Lauro (1996).
A molecular code dictates sequence-specific DNA recognition by homeodomains.
  EMBO J, 15, 4992-5000.  
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.