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protein dna_rna Protein-protein interface(s) links
Transcription/DNA PDB id
1fjl
Jmol
Contents
Protein chains
65 a.a. *
58 a.a. *
59 a.a. *
DNA/RNA
Waters ×243
* Residue conservation analysis
PDB id:
1fjl
Name: Transcription/DNA
Title: Homeodomain from the drosophila paired protein bound to a DNA oligonucleotide
Structure: Paired protein. Chain: a, b, c. Fragment: homeodomain. Synonym: prd, paired protein. Engineered: yes. Mutation: yes. DNA (5'- d( Ap Ap Tp Ap Ap Tp Cp Tp Gp Ap Tp Tp Ap C)-3'). Chain: d.
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.198    
Authors: D.S.Wilson,B.Guenther,C.Desplan,J.Kuriyan
Key ref: D.S.Wilson et al. (1995). High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA. Cell, 82, 709-719. PubMed id: 7671301 DOI: 10.1016/0092-8674(95)90468-9
Date:
17-Dec-95     Release date:   20-Jun-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06601  (PRD_DROME) -  Segmentation protein paired
Seq:
Struc: 		 
Seq:
Struc: 		613 a.a.
65 a.a.*
Protein chain
Pfam   ArchSchema ?
P06601  (PRD_DROME) -  Segmentation protein paired
Seq:
Struc: 		 
Seq:
Struc: 		613 a.a.
58 a.a.*
Protein chain
Pfam   ArchSchema ?
P06601  (PRD_DROME) -  Segmentation protein paired
Seq:
Struc: 		 
Seq:
Struc: 		613 a.a.
59 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     regulation of transcription   2 terms 
  Biochemical function     transcription regulator activity     4 terms  

 

 
DOI no: 10.1016/0092-8674(95)90468-9 Cell 82:709-719 (1995)
PubMed id: 7671301  
 
 
High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA.
D.S.Wilson, B.Guenther, C.Desplan, J.Kuriyan.
 
  ABSTRACT  
 
The crystal structure of the paired homeodomain bound to DNA as a cooperative dimer has been determined to 2.0 A resolution. Direct contacts between each homeodomain and the DNA are similar to those described previously. In addition, an extensive network of water molecules mediates contacts between the recognition helix and the DNA major groove. Several symmetrical contacts between the two homeodomains underlie the cooperative interaction, and deformations in the DNA structure are necessary for the establishment of these contacts. Comparison with structures of homeodomains bound monomerically to DNA suggests that the binding of a single paired homeodomain can introduce these DNA distortions, thus preparing a template for the cooperative interaction with a second homeodomain. This study shows how the paired (Pax) class homeodomains have achieved cooperativity in DNA binding without the assistance of other domains, thereby enabling the recognition of target sequences that are long enough to ensure specificity.
 

Literature references that cite this PDB file's key reference

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PDB codes: 3a01 3a02 3a03 3lnq
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Cdx4 and menin co-regulate Hoxa9 expression in hematopoietic cells.
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PDB codes: 1p7i 1p7j
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PAX6 and congenital eye malformations.
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PDB code: 1qry
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12297046 C.H.Shin, Z.P.Liu, R.Passier, C.L.Zhang, D.Z.Wang, T.M.Harris, H.Yamagishi, J.A.Richardson, G.Childs, and E.N.Olson (2002).
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Pax genes and eye organogenesis.
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11948255 H.Seo, S.J.Hong, S.Guo, H.S.Kim, C.H.Kim, D.Y.Hwang, O.Isacson, A.Rosenthal, and K.S.Kim (2002).
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11867549 M.A.Schumacher, M.C.Miller, S.Grkovic, M.H.Brown, R.A.Skurray, and R.G.Brennan (2002).
Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR.
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PDB code: 1jt0
12011080 P.Melamed, M.Koh, P.Preklathan, L.Bei, and C.Hew (2002).
Multiple mechanisms for Pitx-1 transactivation of a luteinizing hormone beta subunit gene.
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PAX6, paired domain influences sequence recognition by the homeodomain.
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11847127 T.K.Chiu, C.Sohn, R.E.Dickerson, and R.C.Johnson (2002).
Testing water-mediated DNA recognition by the Hin recombinase.
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PDB codes: 1ijw 1jj6 1jj8 1jko 1jkp 1jkq 1jkr
12215455 X.Wang, S.Xu, C.Rivolta, L.Y.Li, G.H.Peng, P.K.Swain, C.H.Sung, A.Swaroop, E.L.Berson, T.P.Dryja, and S.Chen (2002).
Barrier to autointegration factor interacts with the cone-rod homeobox and represses its transactivation function.
  J Biol Chem, 277, 43288-43300.  
11861910 Z.Morávek, S.Neidle, and B.Schneider (2002).
Protein and drug interactions in the minor groove of DNA.
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11748842 C.Rivolta, E.L.Berson, and T.P.Dryja (2001).
Dominant Leber congenital amaurosis, cone-rod degeneration, and retinitis pigmentosa caused by mutant versions of the transcription factor CRX.
  Hum Mutat, 18, 488-498.  
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.  
  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.  
  11738049 T.Nishikawa, H.Okamura, A.Nagadoi, P.König, D.Rhodes, and Y.Nishimura (2001).
Solution structure of a telomeric DNA complex of human TRF1.
  Structure, 9, 1237-1251.
PDB codes: 1ity 1iv6
11027281 C.Zhao, V.Dave, F.Yang, T.Scarborough, and J.Ma (2000).
Target selectivity of bicoid is dependent on nonconsensus site recognition and protein-protein interaction.
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Genetic and biochemical diversity in the Pax gene family.
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Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx.
  Curr Biol, 10, 301-310.  
10889025 R.A.Grant, M.A.Rould, J.D.Klemm, and C.O.Pabo (2000).
Exploring the role of glutamine 50 in the homeodomain-DNA interface: crystal structure of engrailed (Gln50 --> ala) complex at 2.0 A.
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PDB code: 1du0
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The COOH-terminal transactivation domain plays a key role in regulating the in vitro and in vivo function of Pax3 homeodomain.
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The zebrafish bonnie and clyde gene encodes a Mix family homeodomain protein that regulates the generation of endodermal precursors.
  Genes Dev, 14, 1279-1289.  
10592236 Y.Wang, K.J.Addess, L.Geer, T.Madej, A.Marchler-Bauer, D.Zimmerman, and S.H.Bryant (2000).
MMDB: 3D structure data in Entrez.
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Multiprotein-DNA complexes in transcriptional regulation.
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Structure of a HoxB1-Pbx1 heterodimer bound to DNA: role of the hexapeptide and a fourth homeodomain helix in complex formation.
  Cell, 96, 587-597.
PDB code: 1b72
10090291 H.Kono, and A.Sarai (1999).
Structure-based prediction of DNA target sites by regulatory proteins.
  Proteins, 35, 114-131.  
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Phosphorylation of the transactivation domain of Pax6 by extracellular signal-regulated kinase and p38 mitogen-activated protein kinase.
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A conserved blueprint for the eye?
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Structural features of protein-nucleic acid recognition sites.
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10480898 M.D.Galibert, U.Yavuzer, T.J.Dexter, and C.R.Goding (1999).
Pax3 and regulation of the melanocyte-specific tyrosinase-related protein-1 promoter.
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The oncogenic potential of the Pax3-FKHR fusion protein requires the Pax3 homeodomain recognition helix but not the Pax3 paired-box DNA binding domain.
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10542273 S.C.Tucker, and R.Wisdom (1999).
Site-specific heterodimerization by paired class homeodomain proteins mediates selective transcriptional responses.
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The SKN-1 amino-terminal arm is a DNA specificity segment.
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The yeast a1 and alpha2 homeodomain proteins do not contribute equally to heterodimeric DNA binding.
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Partial V(D)J recombination activity leads to Omenn syndrome.
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A structural basis for recognition of A.T and T.A base pairs in the minor groove of B-DNA.
  Science, 282, 111-115.
PDB codes: 407d 408d
9857196 F.X.Gomis-Rüth, M.Solá, P.Acebo, A.Párraga, A.Guasch, R.Eritja, A.González, M.Espinosa, G.del Solar, and M.Coll (1998).
The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator.
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PDB codes: 1b01 2cpg
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Tumor-specific PAX3-FKHR transcription factor, but not PAX3, activates the platelet-derived growth factor alpha receptor.
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Analysis and design of three-stranded coiled coils and three-helix bundles.
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Segmentation: painting stripes from flies to vertebrates.
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The role of homeobox genes in hematopoiesis.
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Solution structure of the cellular factor BAF responsible for protecting retroviral DNA from autointegration.
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PDB codes: 2ezx 2ezy 2ezz
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Cloning of Mix-related homeodomain proteins using fast retrieval of gel shift activities, (FROGS), a technique for the isolation of DNA-binding proteins.
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Alx-4, a transcriptional activator whose expression is restricted to sites of epithelial-mesenchymal interactions.
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NMR structure of a parallel homotrimeric coiled coil.
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PDB code: 1aq5
9811867 S.Jun, R.V.Wallen, A.Goriely, B.Kalionis, and C.Desplan (1998).
Lune/eye gone, a Pax-like protein, uses a partial paired domain and a homeodomain for DNA recognition.
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Site-directed mutations in the vnd/NK-2 homeodomain. Basis of variations in structure and sequence-specific DNA binding.
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Negative autoregulation of the organizer-specific homeobox gene goosecoid.
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Isoforms of hepatocyte nuclear factor-6 differ in DNA-binding properties, contain a bifunctional homeodomain, and define the new ONECUT class of homeodomain proteins.
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9706693 Y.Lan, M.Fujioka, R.Polsgrove, P.Miskiewicz, D.Morrissey, T.Goto, and M.Weir (1998).
Plasticity of Drosophila paired function.
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Reciprocal effect of Waardenburg syndrome mutations on DNA binding by the Pax-3 paired domain and homeodomain.
  Hum Mol Genet, 6, 1781-1790.  
9390563 C.L.Freund, C.Y.Gregory-Evans, T.Furukawa, M.Papaioannou, J.Looser, L.Ploder, J.Bellingham, D.Ng, J.A.Herbrick, A.Duncan, S.W.Scherer, L.C.Tsui, A.Loutradis-Anagnostou, S.G.Jacobson, C.L.Cepko, S.S.Bhattacharya, and R.R.McInnes (1997).
Cone-rod dystrophy due to mutations in a novel photoreceptor-specific homeobox gene (CRX) essential for maintenance of the photoreceptor.
  Cell, 91, 543-553.  
9241421 G.Patikoglou, and S.K.Burley (1997).
Eukaryotic transcription factor-DNA complexes.
  Annu Rev Biophys Biomol Struct, 26, 289-325.  
  9377483 G.Sheng, E.Harris, C.Bertuccioli, and C.Desplan (1997).
Modular organization of Pax/homeodomain proteins in transcriptional regulation.
  Biol Chem, 378, 863-872.  
9312061 G.van Pouderoyen, R.F.Ketting, A.Perrakis, R.H.Plasterk, and T.K.Sixma (1997).
Crystal structure of the specific DNA-binding domain of Tc3 transposase of C.elegans in complex with transposon DNA.
  EMBO J, 16, 6044-6054.
PDB code: 1tc3
9079665 H.Zhong, and A.K.Vershon (1997).
The yeast homeodomain protein MATalpha2 shows extended DNA binding specificity in complex with Mcm1.
  J Biol Chem, 272, 8402-8409.  
9012668 J.H.Carra, and P.L.Privalov (1997).
Energetics of folding and DNA binding of the MAT alpha 2 homeodomain.
  Biochemistry, 36, 526-535.  
9154919 J.M.Gruschus, D.H.Tsao, L.H.Wang, M.Nirenberg, and J.A.Ferretti (1997).
Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity.
  Biochemistry, 36, 5372-5380.
PDB codes: 1nk2 1nk3
9032063 J.W.Schwabe (1997).
The role of water in protein-DNA interactions.
  Curr Opin Struct Biol, 7, 126-134.  
  9343429 K.J.Simon, D.A.Grueneberg, and M.Gilman (1997).
Protein and DNA contact surfaces that mediate the selective action of the Phox1 homeodomain at the c-fos serum response element.
  Mol Cell Biol, 17, 6653-6662.  
9353283 K.J.Vogan, and P.Gros (1997).
The C-terminal subdomain makes an important contribution to the DNA binding activity of the Pax-3 paired domain.
  J Biol Chem, 272, 28289-28295.  
  9309220 L.Tucker-Kellogg, M.A.Rould, K.A.Chambers, S.E.Ades, R.T.Sauer, and C.O.Pabo (1997).
Engrailed (Gln50-->Lys) homeodomain-DNA complex at 1.9 A resolution: structural basis for enhanced affinity and altered specificity.
  Structure, 5, 1047-1054.
PDB code: 2hdd
9365251 M.C.Justice, B.P.Hogan, and A.K.Vershon (1997).
Homeodomain-DNA interactions of the Pho2 protein are promoter-dependent.
  Nucleic Acids Res, 25, 4730-4739.  
9056723 P.Callaerts, G.Halder, and W.J.Gehring (1997).
PAX-6 in development and evolution.
  Annu Rev Neurosci, 20, 483-532.  
9384586 P.Cramer, C.J.Larson, G.L.Verdine, and C.W.Müller (1997).
Structure of the human NF-kappaB p52 homodimer-DNA complex at 2.1 A resolution.
  EMBO J, 16, 7078-7090.
PDB code: 1a3q
9427255 P.K.Swain, S.Chen, Q.L.Wang, L.M.Affatigato, C.L.Coats, K.D.Brady, G.A.Fishman, S.G.Jacobson, A.Swaroop, E.Stone, P.A.Sieving, and D.J.Zack (1997).
Mutations in the cone-rod homeobox gene are associated with the cone-rod dystrophy photoreceptor degeneration.
  Neuron, 19, 1329-1336.  
9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
  Biopolymers, 44, 361-403.  
9174161 R.Gherzi, P.Briata, E.Boncinelli, M.Ponassi, G.Querzè, F.Viti, G.Corte, and L.Zardi (1997).
The human homeodomain protein OTX2 binds to the human tenascin-C promoter and trans-represses its activity in transfected cells.
  DNA Cell Biol, 16, 559-567.  
9013587 Z.P.Xu, and G.F.Saunders (1997).
Transcriptional regulation of the human PAX6 gene promoter.
  J Biol Chem, 272, 3430-3436.  
  8768896 A.K.Vershon (1996).
Protein interactions of homeodomain proteins.
  Curr Opin Biotechnol, 7, 392-396.  
8696974 C.Wolberger (1996).
Homeodomain interactions.
  Curr Opin Struct Biol, 6, 62-68.  
  8791518 D.Engelkamp, and V.van Heyningen (1996).
Transcription factors in disease.
  Curr Opin Genet Dev, 6, 334-342.  
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.  
8692913 D.S.Wilson, G.Sheng, S.Jun, and C.Desplan (1996).
Conservation and diversification in homeodomain-DNA interactions: a comparative genetic analysis.
  Proc Natl Acad Sci U S A, 93, 6886-6891.  
8798534 F.Pio, R.Kodandapani, C.Z.Ni, W.Shepard, M.Klemsz, S.R.McKercher, R.A.Maki, and K.R.Ely (1996).
New insights on DNA recognition by ets proteins from the crystal structure of the PU.1 ETS domain-DNA complex.
  J Biol Chem, 271, 23329-23337.  
  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.  
8913682 H.S.Pappa, A.E.Stewart, and N.Q.McDonald (1996).
Incorporating anomalous scattering centres into macromolecules.
  Curr Opin Struct Biol, 6, 611-616.  
8901570 N.Y.Sidorova, and D.C.Rau (1996).
Differences in water release for the binding of EcoRI to specific and nonspecific DNA sequences.
  Proc Natl Acad Sci U S A, 93, 12272-12277.  
  8591025 T.Tullius (1995).
Homeodomains: together again for the first time.
  Structure, 3, 1143-1145.  
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