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PDBsum entry 1hom

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protein links
DNA-binding protein PDB id
1hom
Jmol
Contents
Protein chain
68 a.a. *
* Residue conservation analysis
PDB id:
1hom
Name: DNA-binding protein
Title: Determination of the three-dimensional structure of the antennapedia homeodomain from drosophila in solution by 1h nuclear magnetic resonance spectroscopy
Structure: Antennapedia protein. Chain: a. Engineered: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Expressed in: escherichia coli. Expression_system_taxid: 562
NMR struc: 19 models
Authors: Y.-Q.Qian,M.Billeter,G.Otting,M.Muller,W.J.Gehring, K.Wuthrich
Key ref: M.Billeter et al. (1990). Determination of the three-dimensional structure of the Antennapedia homeodomain from Drosophila in solution by 1H nuclear magnetic resonance spectroscopy. J Mol Biol, 214, 183-197. PubMed id: 2164583
Date:
08-Oct-91     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02833  (ANTP_DROME) -  Homeotic protein antennapedia
Seq:
Struc:
378 a.a.
68 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!
  Cellular component     nucleus   1 term 
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     DNA binding     3 terms  

 

 
J Mol Biol 214:183-197 (1990)
PubMed id: 2164583  
 
 
Determination of the three-dimensional structure of the Antennapedia homeodomain from Drosophila in solution by 1H nuclear magnetic resonance spectroscopy.
M.Billeter, Y.Qian, G.Otting, M.Müller, W.J.Gehring, K.Wüthrich.
 
  ABSTRACT  
 
The determination of the three-dimensional structure of the Antennapedia homeodomain from Drosophila in solution is described. The techniques used are 1H nuclear magnetic resonance spectroscopy for the data collection, and calculation of the protein structure with the program DISMAN followed by restrained energy minimization with a modified version of the program AMBER. A group of 19 conformers characterizes a well-defined structure for residues 7 to 59, with an average root-mean-square distance from the backbone atoms of 0.6 A relative to the mean of the 19 structures. The structure contains a helix from residues 10 to 21, a helix-turn-helix motif from residues 28 to 52, which is similar to those reported for several prokaryotic repressor proteins, and a somewhat flexible fourth helix from residues 53 to 59, which essentially forms an extension of the presumed recognition helix, residues 42 to 52. The helices enclose a structurally well-defined molecular core of hydrophobic amino acid side-chains.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19343221 M.Gao, and J.Skolnick (2009).
From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions.
  PLoS Comput Biol, 5, e1000341.  
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.  
15705164 M.Saviano, C.Isernia, C.Bassarello, P.Di Lello, S.Galdiero, D.F.Mierke, E.Benedetti, and C.Pedone (2005).
Conformational analysis by NMR and distance geometry techniques of a peptide mimetic of the third helix of the Antennapedia homeodomain.
  J Pept Res, 65, 200-208.  
16075387 Z.N.Akin, and A.J.Nazarali (2005).
Hox genes and their candidate downstream targets in the developing central nervous system.
  Cell Mol Neurobiol, 25, 697-741.  
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
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.  
9671699 M.C.Lo, S.Ha, I.Pelczer, S.Pal, and S.Walker (1998).
The solution structure of the DNA-binding domain of Skn-1.
  Proc Natl Acad Sci U S A, 95, 8455-8460.  
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.  
8898894 G.Esposito, F.Fogolari, G.Damante, S.Formisano, G.Tell, A.Leonardi, R.Di Lauro, and P.Viglino (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.
PDB code: 1ftt
  8844842 P.Luginbühl, J.Wu, O.Zerbe, C.Ortenzi, P.Luporini, and K.Wüthrich (1996).
The NMR solution structure of the pheromone Er-11 from the ciliated protozoan Euplotes raikovi.
  Protein Sci, 5, 1512-1522.
PDB code: 1ery
  7825605 A.K.Lalwani, J.R.Brister, J.Fex, K.M.Grundfast, B.Ploplis, T.B.San Agustin, and E.R.Wilcox (1995).
Further elucidation of the genomic structure of PAX3, and identification of two different point mutations within the PAX3 homeobox that cause Waardenburg syndrome type 1 in two families.
  Am J Hum Genet, 56, 75-83.  
  7910796 D.L.Smith, and A.D.Johnson (1994).
Operator-constitutive mutations in a DNA sequence recognized by a yeast homeodomain.
  EMBO J, 13, 2378-2387.  
7915117 J.H.Kehrl (1994).
Homeobox genes in hematopoiesis.
  Crit Rev Oncol Hematol, 16, 145-156.  
  8264592 M.K.Gross, and P.Gruss (1994).
Functional analysis of mouse Hoxa-7 in Saccharomyces cerevisiae: sequences outside the homeodomain base contact zone influence binding and activation.
  Mol Cell Biol, 14, 238-254.  
  7833811 M.Ottiger, T.Szyperski, P.Luginbühl, C.Ortenzi, P.Luporini, R.A.Bradshaw, and K.Wüthrich (1994).
The NMR solution structure of the pheromone Er-2 from the ciliated protozoan Euplotes raikovi.
  Protein Sci, 3, 1515-1526.
PDB code: 1erd
7909517 M.Seimiya, H.Ishiguro, K.Miura, Y.Watanabe, and Y.Kurosawa (1994).
Homeobox-containing genes in the most primitive metazoa, the sponges.
  Eur J Biochem, 221, 219-225.  
  7833813 P.Luginbühl, M.Ottiger, S.Mronga, and K.Wüthrich (1994).
Structure comparison of the pheromones Er-1, Er-10, and Er-2 from Euplotes raikovi.
  Protein Sci, 3, 1537-1546.  
7915199 S.K.Chan, L.Jaffe, M.Capovilla, J.Botas, and R.S.Mann (1994).
The DNA binding specificity of Ultrabithorax is modulated by cooperative interactions with extradenticle, another homeoprotein.
  Cell, 78, 603-615.  
  7833812 S.Mronga, P.Luginbühl, L.R.Brown, C.Ortenzi, P.Luporini, R.A.Bradshaw, and K.Wüthrich (1994).
The NMR solution structure of the pheromone Er-1 from the ciliated protozoan Euplotes raikovi.
  Protein Sci, 3, 1527-1536.
PDB code: 1erc
  7987224 T.Liu, E.F.DeRose, and G.P.Mullen (1994).
Determination of the structure of the DNA binding domain of gamma delta resolvase in solution.
  Protein Sci, 3, 1286-1295.
PDB codes: 1res 1ret
8044836 W.J.Gehring, Y.Q.Qian, M.Billeter, K.Furukubo-Tokunaga, A.F.Schier, D.Resendez-Perez, M.Affolter, G.Otting, and K.Wüthrich (1994).
Homeodomain-DNA recognition.
  Cell, 78, 211-223.  
7909611 Y.Q.Qian, D.Resendez-Perez, W.J.Gehring, and K.Wüthrich (1994).
The des(1-6)antennapedia homeodomain: comparison of the NMR solution structure and the DNA-binding affinity with the intact Antennapedia homeodomain.
  Proc Natl Acad Sci U S A, 91, 4091-4095.
PDB code: 1san
  8491172 B.Leiting, R.De Francesco, L.Tomei, R.Cortese, G.Otting, and K.Wüthrich (1993).
The three-dimensional NMR-solution structure of the polypeptide fragment 195-286 of the LFB1/HNF1 transcription factor from rat liver comprises a nonclassical homeodomain.
  EMBO J, 12, 1797-1803.  
8255758 L.Cavarec, and T.Heidmann (1993).
The Drosophila copia retrotransposon contains binding sites for transcriptional regulation by homeoproteins.
  Nucleic Acids Res, 21, 5041-5049.  
8229096 M.J.Sippl (1993).
Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures.
  J Comput Aided Mol Des, 7, 473-501.  
8290361 M.P.Laget, I.Callebaut, Y.de Launoit, D.Stehelin, and J.P.Mornon (1993).
Predicted common structural features of DNA-binding domains from Ets, Myb and HMG transcription factors.
  Nucleic Acids Res, 21, 5987-5996.  
8272423 M.W.MacArthur, and J.M.Thornton (1993).
Conformational analysis of protein structures derived from NMR data.
  Proteins, 17, 232-251.  
  1346762 A.Dorn, M.Affolter, M.Müller, W.J.Gehring, and W.Leupin (1992).
Distamycin-induced inhibition of homeodomain-DNA complexes.
  EMBO J, 11, 279-286.  
  1356766 L.Tomei, R.Cortese, and R.De Francesco (1992).
A POU-A related region dictates DNA binding specificity of LFB1/HNF1 by orienting the two XL-homeodomains in the dimer.
  EMBO J, 11, 4119-4129.  
  1304339 T.H.Xia, J.H.Bushweller, P.Sodano, M.Billeter, O.Björnberg, A.Holmgren, and K.Wüthrich (1992).
NMR structure of oxidized Escherichia coli glutaredoxin: comparison with reduced E. coli glutaredoxin and functionally related proteins.
  Protein Sci, 1, 310-321.
PDB codes: 1ego 1grx
1359544 Y.Q.Qian, G.Otting, K.Furukubo-Tokunaga, M.Affolter, W.J.Gehring, and K.Wüthrich (1992).
NMR structure determination reveals that the homeodomain is connected through a flexible linker to the main body in the Drosophila Antennapedia protein.
  Proc Natl Acad Sci U S A, 89, 10738-10742.  
1686166 D.J.Wolgemuth, C.M.Viviano, and F.Watrin (1991).
Expression of homeobox genes during spermatogenesis.
  Ann N Y Acad Sci, 637, 300-312.  
  1989879 J.Vendrell, M.Billeter, G.Wider, F.X.Avilés, and K.Wüthrich (1991).
The NMR structure of the activation domain isolated from porcine procarboxypeptidase B.
  EMBO J, 10, 11-15.
PDB code: 1pba
2001587 M.Affolter, A.Percival-Smith, M.Müller, M.Billeter, Y.Q.Qian, G.Otting, K.Wüthrich, and W.J.Gehring (1991).
Similarities between the homeodomain and the Hin recombinase DNA-binding domain.
  Cell, 64, 879-880.  
1841711 P.Güntert, and K.Wüthrich (1991).
Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints.
  J Biomol NMR, 1, 447-456.  
  1979032 A.Percival-Smith, M.Müller, M.Affolter, and W.J.Gehring (1990).
The interaction with DNA of wild-type and mutant fushi tarazu homeodomains.
  EMBO J, 9, 3967-3974.  
  1976507 G.Otting, Y.Q.Qian, M.Billeter, M.Müller, M.Affolter, W.J.Gehring, and K.Wüthrich (1990).
Protein--DNA contacts in the structure of a homeodomain--DNA complex determined by nuclear magnetic resonance spectroscopy in solution.
  EMBO J, 9, 3085-3092.  
1979524 S.Hayashi, and M.P.Scott (1990).
What determines the specificity of action of Drosophila homeodomain proteins?
  Cell, 63, 883-894.  
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.