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Transcription/DNA PDB id
1hdd
Jmol
Contents
Protein chains
57 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
1hdd
Name: Transcription/DNA
Title: Crystal structure of an engrailed homeodomain-DNA complex at 2.8 angstroms resolution: a framework for understanding homeodomain-DNA interactions
Structure: DNA (5'- d( Tp Tp Tp Tp Gp Cp Cp Ap Tp Gp Tp Ap Ap Tp Tp Ap C p Cp Tp Ap A)-3'). Chain: a. Engineered: yes. DNA (5'- d( Ap Tp Tp Ap Gp Gp Tp Ap Ap Tp Tp Ap Cp Ap Tp Gp G p Cp Ap Ap A)-3'). Chain: b.
Source: Synthetic: yes. Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.80Å     R-factor:   0.225    
Authors: C.R.Kissinger,B.Liu,E.Martin-Blanco,T.B.Kornberg C.O.Pabo
Key ref: C.R.Kissinger et al. (1990). Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions. Cell, 63, 579-590. PubMed id: 1977522 DOI: 10.1016/0092-8674(90)90453-L
Date:
16-Sep-91     Release date:   15-Jan-92    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P02836  (HMEN_DROME) -  Segmentation polarity homeobox protein engrailed
Seq:
Struc: 		 
Seq:
Struc: 		552 a.a.
57 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 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     5 terms  

 

 
DOI no: 10.1016/0092-8674(90)90453-L Cell 63:579-590 (1990)
PubMed id: 1977522  
 
 
Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions.
C.R.Kissinger, B.S.Liu, E.Martin-Blanco, T.B.Kornberg, C.O.Pabo.
 
  ABSTRACT  
 
The crystal structure of a complex containing the engrailed homeodomain and a duplex DNA site has been determined at 2.8 A resolution and refined to a crystallographic R factor of 24.4%. In this complex, two separate regions of the 61 amino acid polypeptide contact a TAAT subsite. An N-terminal arm fits into the minor groove, and the side chains of Arg-3 and Arg-5 make contacts near the 5' end of this "core consensus" binding site. An alpha helix fits into the major groove, and the side chains of IIe-47 and Asn-51 contact base pairs near the 3' end of the TAAT site. This "recognition helix" is part of a structurally conserved helix-turn-helix unit, but these helices are longer than the corresponding helices in the lambda repressor, and the relationship between the helix-turn-helix unit and the DNA is significantly different.
 

Literature references that cite this PDB file's key reference

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Molecular regulation of mullerian development by Hox genes.
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Midbrain dopaminergic neurons: control of their cell fate by the engrailed transcription factors.
  Cell Tissue Res, 318, 53-61.  
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A phage display selection of engrailed homeodomain mutants and the importance of residue Q50.
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  Mol Cell Biol, 24, 3827-3837.  
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  Protein Sci, 12, 306-312.
PDB codes: 1mh3 1mh4
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PDB codes: 1p7i 1p7j
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Redox regulation of plant homeodomain transcription factors.
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Structural and thermodynamic characterization of the DNA binding properties of a triple alanine mutant of MATalpha2.
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PDB code: 1le8
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PDB code: 1kqq
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Structure of the DNA binding region of prospero reveals a novel homeo-prospero domain.
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PDB code: 1mij
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Diabetes mutations delineate an atypical POU domain in HNF-1alpha.
  Mol Cell, 10, 1129-1137.
PDB code: 1ic8
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Role of salt bridges in homeodomains investigated by structural analyses and molecular dynamics simulations.
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Structural determinants of ligand binding selectivity between the peroxisome proliferator-activated receptors.
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PDB codes: 1k74 1k7l
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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.
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Electrospray ionization mass spectrometry of oligonucleotide complexes with drugs, metals, and proteins.
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Functional interaction of Jun and homeodomain proteins.
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Evx1 is a postmitotic determinant of v0 interneuron identity in the spinal cord.
  Neuron, 29, 385-399.  
11470884 S.Banerjee-Basu, and A.D.Baxevanis (2001).
Molecular evolution of the homeodomain family of transcription factors.
  Nucleic Acids Res, 29, 3258-3269.  
11125116 S.Banerjee-Basu, D.W.Sink, and A.D.Baxevanis (2001).
The Homeodomain Resource: sequences, structures, DNA binding sites and genomic information.
  Nucleic Acids Res, 29, 291-293.  
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Solution structure of a telomeric DNA complex of human TRF1.
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PDB codes: 1ity 1iv6
11238372 W.Ross, A.Ernst, and R.L.Gourse (2001).
Fine structure of E. coli RNA polymerase-promoter interactions: alpha subunit binding to the UP element minor groove.
  Genes Dev, 15, 491-506.  
10835358 D.E.Rincón-Limas, C.H.Lu, I.Canal, and J.Botas (2000).
The level of DLDB/CHIP controls the activity of the LIM homeodomain protein apterous: evidence for a functional tetramer complex in vivo.
  EMBO J, 19, 2602-2614.  
10749657 D.M.Hagan, A.J.Ross, T.Strachan, S.A.Lynch, V.Ruiz-Perez, Y.M.Wang, P.Scambler, E.Custard, W.Reardon, S.Hassan, P.Nixon, C.Papapetrou, R.M.Winter, Y.Edwards, K.Morrison, M.Barrow, M.P.Cordier-Alex, P.Correia, P.A.Galvin-Parton, S.Gaskill, K.J.Gaskin, S.Garcia-Minaur, R.Gereige, R.Hayward, and T.Homfray (2000).
Mutation analysis and embryonic expression of the HLXB9 Currarino syndrome gene.
  Am J Hum Genet, 66, 1504-1515.  
11252562 J.M.Gibert, E.Mouchel-Vielh, E.Quéinnec, and J.S.Deutsch (2000).
Barnacle duplicate engrailed genes: divergent expression patterns and evidence for a vestigial abdomen.
  Evol Dev, 2, 194-202.  
  11058088 J.T.Bryan, and M.I.Morasso (2000).
The Dlx3 protein harbors basic residues required for nuclear localization, transcriptional activity and binding to Msx1.
  J Cell Sci, 113, 4013-4023.  
  10892804 K.Raha, A.M.Wollacott, M.J.Italia, and J.R.Desjarlais (2000).
Prediction of amino acid sequence from structure.
  Protein Sci, 9, 1106-1119.  
11003645 M.Kipp, F.Göhring, T.Ostendorp, C.M.van Drunen, R.van Driel, M.Przybylski, and F.O.Fackelmayer (2000).
SAF-Box, a conserved protein domain that specifically recognizes scaffold attachment region DNA.
  Mol Cell Biol, 20, 7480-7489.  
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.
  Biochemistry, 39, 8187-8192.
PDB code: 1du0
10799563 R.G.Mirmira, H.Watada, and M.S.German (2000).
Beta-cell differentiation factor Nkx6.1 contains distinct DNA binding interference and transcriptional repression domains.
  J Biol Chem, 275, 14743-14751.  
10592263 S.Banerjee-Basu, J.F.Ryan, and A.D.Baxevanis (2000).
The homeodomain resource: a prototype database for a large protein family.
  Nucleic Acids Res, 28, 329-330.  
10727231 S.Deb, S.Bandyopadhyay, and S.Roy (2000).
DNA sequence dependent and independent conformational changes in multipartite operator recognition by lambda-repressor.
  Biochemistry, 39, 3377-3383.  
11003663 V.Dave, C.Zhao, F.Yang, C.S.Tung, and J.Ma (2000).
Reprogrammable recognition codes in bicoid homeodomain-DNA interaction.
  Mol Cell Biol, 20, 7673-7684.  
  10817762 Y.Kikuchi, L.A.Trinh, J.F.Reiter, J.Alexander, D.Yelon, and D.Y.Stainier (2000).
The zebrafish bonnie and clyde gene encodes a Mix family homeodomain protein that regulates the generation of endodermal precursors.
  Genes Dev, 14, 1279-1289.  
10410794 C.Wolberger (1999).
Multiprotein-DNA complexes in transcriptional regulation.
  Annu Rev Biophys Biomol Struct, 28, 29-56.  
10052460 D.E.Piper, A.H.Batchelor, C.P.Chang, M.L.Cleary, and C.Wolberger (1999).
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
10543441 D.Mennerich, S.Hoffmann, T.Hadrys, H.H.Arnold, and E.Bober (1999).
Two highly related homeodomain proteins, Nkx5-1 and Nkx5-2, display different DNA binding specificities.
  Biol Chem, 380, 1041-1048.  
10673033 H.C.Seo, F.Nilsen, and A.Fjose (1999).
Three structurally and functionally conserved Hlx genes in zebrafish.
  Biochim Biophys Acta, 1489, 323-335.  
  10398683 H.D.Ryoo, and R.S.Mann (1999).
The control of trunk Hox specificity and activity by Extradenticle.
  Genes Dev, 13, 1704-1716.  
  10346815 H.E.Xu, M.A.Rould, W.Xu, J.A.Epstein, R.L.Maas, and C.O.Pabo (1999).
Crystal structure of the human Pax6 paired domain-DNA complex reveals specific roles for the linker region and carboxy-terminal subdomain in DNA binding.
  Genes Dev, 13, 1263-1275.
PDB code: 6pax
10026283 K.Nadassy, S.J.Wodak, and J.Janin (1999).
Structural features of protein-nucleic acid recognition sites.
  Biochemistry, 38, 1999-2017.  
  10523646 K.Shanmugam, N.C.Green, I.Rambaldi, H.U.Saragovi, and M.S.Featherstone (1999).
PBX and MEIS as non-DNA-binding partners in trimeric complexes with HOX proteins.
  Mol Cell Biol, 19, 7577-7588.  
10502778 S.Banerjee-Basu, and A.D.Baxevanis (1999).
Threading analysis of the Pitx2 homeodomain: predicted structural effects of mutations causing Rieger syndrome and iridogoniodysgenesis.
  Hum Mutat, 14, 312-319.  
10542273 S.C.Tucker, and R.Wisdom (1999).
Site-specific heterodimerization by paired class homeodomain proteins mediates selective transcriptional responses.
  J Biol Chem, 274, 32325-32332.  
10666584 S.DeWees, and J.H.Geiger (1999).
Structural studies of the Msx-1 homeodomain-DNA complex I.
  Acta Crystallogr D Biol Crystallogr, 55, 2039-2040.  
  10082571 T.Kophengnavong, A.S.Carroll, and T.K.Blackwell (1999).
The SKN-1 amino-terminal arm is a DNA specificity segment.
  Mol Cell Biol, 19, 3039-3050.  
  9858582 Y.Jin, H.Zhong, and A.K.Vershon (1999).
The yeast a1 and alpha2 homeodomain proteins do not contribute equally to heterodimeric DNA binding.
  Mol Cell Biol, 19, 585-593.  
10536059 Z.Hao, J.Yeung, L.Wolf, R.Doucette, and A.Nazarali (1999).
Differential expression of Hoxa-2 protein along the dorsal-ventral axis of the developing and adult mouse spinal cord.
  Dev Dyn, 216, 201-217.  
9844025 A.Sundås-Larsson, M.Svenson, H.Liao, and P.Engström (1998).
A homeobox gene with potential developmental control function in the meristem of the conifer Picea abies.
  Proc Natl Acad Sci U S A, 95, 15118-15122.  
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.  
9723177 H.G.Belting, C.S.Shashikant, and F.H.Ruddle (1998).
Multiple phases of expression and regulation of mouse Hoxc8 during early embryogenesis.
  J Exp Zool, 282, 196-222.  
9451007 J.Iwahara, T.Kigawa, K.Kitagawa, H.Masumoto, T.Okazaki, and S.Yokoyama (1998).
A helix-turn-helix structure unit in human centromere protein B (CENP-B).
  EMBO J, 17, 827-837.
PDB code: 1bw6
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.  
9788911 J.Woda, B.Schneider, K.Patel, K.Mistry, and H.M.Berman (1998).
An analysis of the relationship between hydration and protein-DNA interactions.
  Biophys J, 75, 2170-2177.  
9452487 L.Huang, N.Grammatikakis, and B.P.Toole (1998).
Organization of the chick CDC37 gene.
  J Biol Chem, 273, 3598-3603.  
9774480 M.Lehmann, T.Siegmund, K.G.Lintermann, and G.Korge (1998).
The pipsqueak protein of Drosophila melanogaster binds to GAGA sequences through a novel DNA-binding domain.
  J Biol Chem, 273, 28504-28509.  
9649440 N.Serrano, and F.Maschat (1998).
Molecular mechanism of polyhomeotic activation by Engrailed.
  EMBO J, 17, 3704-3713.  
9628487 P.B.Rupert, G.W.Daughdrill, B.Bowerman, and B.W.Matthews (1998).
A new DNA-binding motif in the Skn-1 binding domain-DNA complex.
  Nat Struct Biol, 5, 484-491.
PDB code: 1skn
9512546 P.König, L.Fairall, and D.Rhodes (1998).
Sequence-specific DNA recognition by the myb-like domain of the human telomere binding protein TRF1: a model for the protein-DNA complex.
  Nucleic Acids Res, 26, 1731-1740.  
  9819426 P.Sauter, and P.Matthias (1998).
Coactivator OBF-1 makes selective contacts with both the POU-specific domain and the POU homeodomain and acts as a molecular clamp on DNA.
  Mol Cell Biol, 18, 7397-7409.  
  9774673 S.A.Valentine, G.Chen, T.Shandala, J.Fernandez, S.Mische, R.Saint, and A.J.Courey (1998).
Dorsal-mediated repression requires the formation of a multiprotein repression complex at the ventral silencer.
  Mol Cell Biol, 18, 6584-6594.  
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.  
  9739097 T.Nishikawa, A.Nagadoi, S.Yoshimura, S.Aimoto, and Y.Nishimura (1998).
Solution structure of the DNA-binding domain of human telomeric protein, hTRF1.
  Structure, 6, 1057-1065.
PDB code: 1ba5
9706693 Y.Lan, M.Fujioka, R.Polsgrove, P.Miskiewicz, D.Morrissey, T.Goto, and M.Weir (1998).
Plasticity of Drosophila paired function.
  Dev Genet, 23, 45-55.  
9207034 A.G.Stepchenko, N.N.Luchina, and E.V.Pankratova (1997).
Cysteine 50 of the POU H domain determines the range of targets recognized by POU proteins.
  Nucleic Acids Res, 25, 2847-2853.  
9235002 A.L.Lomize, and H.I.Mosberg (1997).
Thermodynamic model of secondary structure for alpha-helical peptides and proteins.
  Biopolymers, 42, 239-269.  
  9279758 A.P.Read, and V.E.Newton (1997).
Waardenburg syndrome.
  J Med Genet, 34, 656-665.  
  9303538 A.S.Carroll, D.E.Gilbert, X.Liu, J.W.Cheung, J.E.Michnowicz, G.Wagner, T.E.Ellenberger, and T.K.Blackwell (1997).
SKN-1 domain folding and basic region monomer stabilization upon DNA binding.
  Genes Dev, 11, 2227-2238.  
9302254 A.S.Fortin, D.A.Underhill, and P.Gros (1997).
Reciprocal effect of Waardenburg syndrome mutations on DNA binding by the Pax-3 paired domain and homeodomain.
  Hum Mol Genet, 6, 1781-1790.  
  9215898 C.Benassayag, M.Boube, L.Seroude, and D.L.Cribbs (1997).
Point mutations within and outside the homeodomain identify sequences required for proboscipedia homeotic function in Drosophila.
  Genetics, 146, 939-949.  
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.  
9360601 C.Y.Chien, R.Tejero, Y.Huang, D.E.Zimmerman, C.B.Ríos, R.M.Krug, and G.T.Montelione (1997).
A novel RNA-binding motif in influenza A virus non-structural protein 1.
  Nat Struct Biol, 4, 891-895.
PDB code: 1ns1
9122247 F.S.Jones, C.Kioussi, D.W.Copertino, P.Kallunki, B.D.Holst, and G.M.Edelman (1997).
Barx2, a new homeobox gene of the Bar class, is expressed in neural and craniofacial structures during development.
  Proc Natl Acad Sci U S A, 94, 2632-2637.  
9241421 G.Patikoglou, and S.K.Burley (1997).
Eukaryotic transcription factor-DNA complexes.
  Annu Rev Biophys Biomol Struct, 26, 289-325.  
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
  9144767 H.Li, R.Tejero, D.Monleon, D.Bassolino-Klimas, C.Abate-Shen, R.E.Bruccoleri, and G.T.Montelione (1997).
Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: application in predicting the three-dimensional structure of murine homeodomain Msx-1.
  Protein Sci, 6, 956-970.  
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.  
9360602 J.Liu, P.A.Lynch, C.Y.Chien, G.T.Montelione, R.M.Krug, and H.M.Berman (1997).
Crystal structure of the unique RNA-binding domain of the influenza virus NS1 protein.
  Nat Struct Biol, 4, 896-899.
PDB code: 1ail
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
  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.  
9228093 K.Shanmugam, M.S.Featherstone, and H.U.Saragovi (1997).
Residues flanking the HOX YPWM motif contribute to cooperative interactions with PBX.
  J Biol Chem, 272, 19081-19087.  
9111059 L.A.Dickinson, C.D.Dickinson, and T.Kohwi-Shigematsu (1997).
An atypical homeodomain in SATB1 promotes specific recognition of the key structural element in a matrix attachment region.
  J Biol Chem, 272, 11463-11470.  
9354759 L.Jen-Jacobson (1997).
Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state.
  Biopolymers, 44, 153-180.  
9188697 L.Li, and K.S.Matthews (1997).
Differences in water release with DNA binding by ultrabithorax and deformed homeodomains.
  Biochemistry, 36, 7003-7011.  
  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
8989327 M.A.Markus, A.P.Hinck, S.Huang, D.E.Draper, and D.A.Torchia (1997).
High resolution solution structure of ribosomal protein L11-C76, a helical protein with a flexible loop that becomes structured upon binding to RNA.
  Nat Struct Biol, 4, 70-77.
PDB codes: 1fow 1fox
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.  
9228950 M.Cai, R.Zheng, M.Caffrey, R.Craigie, G.M.Clore, and A.M.Gronenborn (1997).
Solution structure of the N-terminal zinc binding domain of HIV-1 integrase.
  Nat Struct Biol, 4, 567-577.
PDB codes: 1wja 1wjb 1wjc 1wjd
9218422 M.Oda, K.Furukawa, K.Ogata, A.Sarai, S.Ishii, Y.Nishimura, and H.Nakamura (1997).
Investigation of the pyrimidine preference by the c-Myb DNA-binding domain at the initial base of the consensus sequence.
  J Biol Chem, 272, 17966-17971.  
  9300483 M.Schmiedeskamp, P.Rajagopal, and R.E.Klevit (1997).
NMR chemical shift perturbation mapping of DNA binding by a zinc-finger domain from the yeast transcription factor ADR1.
  Protein Sci, 6, 1835-1848.  
9369471 M.Schmiedeskamp, and R.E.Klevit (1997).
Paramagnetic cobalt as a probe of the orientation of an accessory DNA-binding region of the yeast ADR1 zinc-finger protein.
  Biochemistry, 36, 14003-14011.  
  9371644 N.Turque, S.Plaza, K.H.Klempnauer, and S.Saule (1997).
Overexpression of A-myb induces basic fibroblast growth factor-dependent proliferation of chicken neuroretina cells.
  J Virol, 71, 9778-9781.  
9384588 P.C.Shah, E.Bertolino, and H.Singh (1997).
Using altered specificity Oct-1 and Oct-2 mutants to analyze the regulation of immunoglobulin gene transcription.
  EMBO J, 16, 7105-7117.  
9056723 P.Callaerts, G.Halder, and W.J.Gehring (1997).
PAX-6 in development and evolution.
  Annu Rev Neurosci, 20, 483-532.  
9048479 P.König, and D.Rhodes (1997).
Recognition of telomeric DNA.
  Trends Biochem Sci, 22, 43-47.  
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.  
  9083114 R.M.Xu, C.Koch, Y.Liu, J.R.Horton, D.Knapp, K.Nasmyth, and X.Cheng (1997).
Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell-cycle control of DNA synthesis.
  Structure, 5, 349-358.
PDB code: 1bm8
8989317 Y.Xing, D.Guha Thakurta, and D.E.Draper (1997).
The RNA binding domain of ribosomal protein L11 is structurally similar to homeodomains.
  Nat Struct Biol, 4, 24-27.  
9261149 Z.Ge, N.W.Chan, M.M.Palcic, and D.E.Taylor (1997).
Cloning and heterologous expression of an alpha1,3-fucosyltransferase gene from the gastric pathogen Helicobacter pylori.
  J Biol Chem, 272, 21357-21363.  
8667990 A.K.Lalwani, A.N.Mhatre, T.B.San Agustin, and E.R.Wilcox (1996).
Genotype-phenotype correlations in type 1 Waardenburg syndrome.
  Laryngoscope, 106, 895-902.  
  8768896 A.K.Vershon (1996).
Protein interactions of homeodomain proteins.
  Curr Opin Biotechnol, 7, 392-396.  
  8889542 A.R.Mushegian, and E.V.Koonin (1996).
Sequence analysis of eukaryotic developmental proteins: ancient and novel domains.
  Genetics, 144, 817-828.  
8702862 A.Zhu, and M.A.Kuziora (1996).
Homeodomain interaction with the beta subunit of the general transcription factor TFIIE.
  J Biol Chem, 271, 20993-20996.  
8605297 B.Klinge, B.Uberlacker, C.Korfhage, and W.Werr (1996).
ZmHox: a novel class of maize homeobox genes.
  Plant Mol Biol, 30, 439-453.  
8943214 C.J.Bieberich, K.Fujita, W.W.He, and G.Jay (1996).
Prostate-specific and androgen-dependent expression of a novel homeobox gene.
  J Biol Chem, 271, 31779-31782.  
  8657149 C.P.Chang, L.Brocchieri, W.F.Shen, C.Largman, and M.L.Cleary (1996).
Pbx modulation of Hox homeodomain amino-terminal arms establishes different DNA-binding specificities across the Hox locus.
  Mol Cell Biol, 16, 1734-1745.  
8696974 C.Wolberger (1996).
Homeodomain interactions.
  Curr Opin Struct Biol, 6, 62-68.  
  8887666 C.Y.Chen, and R.J.Schwartz (1996).
Recruitment of the tinman homolog Nkx-2.5 by serum response factor activates cardiac alpha-actin gene transcription.
  Mol Cell Biol, 16, 6372-6384.  
  9000009 D.A.Erlanson, M.Chytil, and G.L.Verdine (1996).
The leucine zipper domain controls the orientation of AP-1 in the NFAT.AP-1.DNA complex.
  Chem Biol, 3, 981-991.  
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.  
8702955 D.Yuan, X.Ma, and J.Ma (1996).
Sequences outside the homeodomain of bicoid are required for protein-protein interaction.
  J Biol Chem, 271, 21660-21665.  
8986770 E.E.Turner (1996).
Similar DNA recognition properties of alternatively spliced Drosophila POU factors.
  Proc Natl Acad Sci U S A, 93, 15097-15101.  
8663425 E.Sock, J.Enderich, M.G.Rosenfeld, and M.Wegner (1996).
Identification of the nuclear localization signal of the POU domain protein Tst-1/Oct6.
  J Biol Chem, 271, 17512-17518.  
  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.  
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
8703957 L.Li, D.von Kessler, P.A.Beachy, and K.S.Matthews (1996).
pH-dependent enhancement of DNA binding by the ultrabithorax homeodomain.
  Biochemistry, 35, 9832-9839.  
8616227 L.Meisel, and E.Lam (1996).
The conserved ELK-homeodomain of KNOTTED-1 contains two regions that signal nuclear localization.
  Plant Mol Biol, 30, 1.  
8882492 M.Friedman-Einat, P.Einat, M.Snyder, and F.Ruddle (1996).
Target gene identification: target specific transcriptional activation by three murine homeodomain/VP16 hybrid proteins in Saccharomyces cerevisiae.
  J Exp Zool, 274, 145-156.  
8620531 P.Konig, R.Giraldo, L.Chapman, and D.Rhodes (1996).
The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA.
  Cell, 85, 125-136.
PDB code: 1ign
8710498 P.S.Knoepfler, Q.Lu, and M.P.Kamps (1996).
Pbx-1 Hox heterodimers bind DNA on inseparable half-sites that permit intrinsic DNA binding specificity of the Hox partner at nucleotides 3' to a TAAT motif.
  Nucleic Acids Res, 24, 2288-2294.  
  8657138 Q.Lu, and M.P.Kamps (1996).
Structural determinants within Pbx1 that mediate cooperative DNA binding with pentapeptide-containing Hox proteins: proposal for a model of a Pbx1-Hox-DNA complex.
  Mol Cell Biol, 16, 1632-1640.  
8761990 R.F.Bulleit, X.Lin, and J.V.Jeppi (1996).
A novel gene selectively expressed in the cerebellum.
  Neurosci Lett, 209, 93-96.  
8948638 S.Barbarić, M.Münsterkötter, J.Svaren, and W.Hörz (1996).
The homeodomain protein Pho2 and the basic-helix-loop-helix protein Pho4 bind DNA cooperatively at the yeast PHO5 promoter.
  Nucleic Acids Res, 24, 4479-4486.  
8798433 S.E.Quaggin, G.B.Heuvel, K.Golden, R.Bodmer, and P.Igarashi (1996).
Primary structure, neural-specific expression, and chromosomal localization of Cux-2, a second murine homeobox gene related to Drosophila cut.
  J Biol Chem, 271, 22624-22634.  
  8665855 S.K.Chan, H.Pöpperl, R.Krumlauf, and R.S.Mann (1996).
An extradenticle-induced conformational change in a HOX protein overcomes an inhibitory function of the conserved hexapeptide motif.
  EMBO J, 15, 2476-2487.  
8643557 S.K.Chan, and R.S.Mann (1996).
A structural model for a homeotic protein-extradenticle-DNA complex accounts for the choice of HOX protein in the heterodimer.
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Double agent: translational regulation by a transcription factor.
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8943030 T.E.Haerry, and W.J.Gehring (1996).
Intron of the mouse Hoxa-7 gene contains conserved homeodomain binding sites that can function as an enhancer element in Drosophila.
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  8890171 V.Zappavigna, L.Falciola, M.Helmer-Citterich, F.Mavilio, and M.E.Bianchi (1996).
HMG1 interacts with HOX proteins and enhances their DNA binding and transcriptional activation.
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8600458 W.F.Shen, C.P.Chang, S.Rozenfeld, G.Sauvageau, R.K.Humphries, M.Lu, H.J.Lawrence, M.L.Cleary, and C.Largman (1996).
Hox homeodomain proteins exhibit selective complex stabilities with Pbx and DNA.
  Nucleic Acids Res, 24, 898-906.  
  7600995 A.John, S.T.Smith, and J.B.Jaynes (1995).
Inserting the Ftz homeodomain into engrailed creates a dominant transcriptional repressor that specifically turns off Ftz target genes in vivo.
  Development, 121, 1801-1813.  
  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.
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The T protein encoded by Brachyury is a tissue-specific transcription factor.
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7625690 A.Klug (1995).
Gene regulatory proteins and their interaction with DNA.
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7582962 A.Rodger, S.Taylor, G.Adlam, I.S.Blagbrough, and I.S.Haworth (1995).
Multiple DNA binding modes of anthracene-9-carbonyl-N1-spermine.
  Bioorg Med Chem, 3, 861-872.  
8532535 B.J.Reardon, D.Gordon, M.J.Ballard, and E.Winter (1995).
DNA binding properties of the Saccharomyces cerevisiae DAT1 gene product.
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  8563624 C.Q.Pan, R.Landgraf, and D.S.Sigman (1995).
Drosophila engrailed-1,10-phenanthroline chimeras as probes of homeodomain-DNA complexes.
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7797561 C.Y.Chen, and R.J.Schwartz (1995).
Identification of novel DNA binding targets and regulatory domains of a murine tinman homeodomain factor, nkx-2.5.
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Sequence-specific targeting of nuclear signal transduction pathways by homeodomain proteins.
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7739902 D.L.Smith, A.B.Desai, and A.D.Johnson (1995).
DNA bending by the a1 and alpha 2 homeodomain proteins from yeast.
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7671301 D.S.Wilson, B.Guenther, C.Desplan, and J.Kuriyan (1995).
High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA.
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PDB code: 1fjl
7664107 D.Stanojevic, and G.L.Verdine (1995).
Deconstruction of GCN4/GCRE into a monomeric peptide-DNA complex.
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7540284 E.C.LaCasse, and Y.A.Lefebvre (1995).
Nuclear localization signals overlap DNA- or RNA-binding domains in nucleic acid-binding proteins.
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7846045 F.B.Johnson, E.Parker, and M.A.Krasnow (1995).
Extradenticle protein is a selective cofactor for the Drosophila homeotics: role of the homeodomain and YPWM amino acid motif in the interaction.
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Identification of target genes regulated by homeotic proteins in Drosophila melanogaster through genetic selection of Ultrabithorax protein-binding sites in yeast.
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The expression pattern of the murine Hoxa-10 gene and the sequence recognition of its homeodomain reveal specific properties of Abdominal B-like genes.
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7784431 J.A.Hirsch, and A.K.Aggarwal (1995).
Purification, crystallization, and preliminary X-ray diffraction analysis of even-skipped homeodomain complexed to DNA.
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Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity.
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PDB code: 1jgg
7716167 J.Janin (1995).
Elusive affinities.
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7568211 J.L.Pomerantz, C.O.Pabo, and P.A.Sharp (1995).
Analysis of homeodomain function by structure-based design of a transcription factor.
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In vivo mutational analysis of the DNA binding domain of the tissue-specific transcription factor, Pit-1.
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Expression of pax-6 during urodele eye development and lens regeneration.
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Hydrogen bonding motifs of protein side chains: descriptions of binding of arginine and amide groups.
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7629095 L.Zulianello, P.van Ulsen, P.van de Putte, and N.Goosen (1995).
Participation of the flank regions of the integration host factor protein in the specificity and stability of DNA binding.
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7647248 M.A.Young, G.Ravishanker, D.L.Beveridge, and H.M.Berman (1995).
Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes.
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The solution structure of the human ETS1-DNA complex reveals a novel mode of binding and true side chain intercalation.
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PDB codes: 1stt 1stw
7744853 M.I.Arnone, M.Zannini, and R.Di Lauro (1995).
The DNA binding activity and the dimerization ability of the thyroid transcription factor I are redox regulated.
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Sequence-specific DNA binding by covalently constrained peptide dimers of the basic leucine zipper protein GCN4.
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8749848 M.Suzuki, and M.Gerstein (1995).
Binding geometry of alpha-helices that recognize DNA.
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Stereochemical basis of DNA bending by transcription factors.
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Covariation of residues in the homeodomain sequence family.
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DNA-binding specificity of the cut repeats from the human cut-like protein.
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7576194 R.Hromas, and R.Costa (1995).
The hepatocyte nuclear factor-3/forkhead transcription regulatory family in development, inflammation, and neoplasia.
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7784225 R.S.Devon, D.J.Porteous, and A.J.Brookes (1995).
Splinkerettes--improved vectorettes for greater efficiency in PCR walking.
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The specificity of homeotic gene function.
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7719857 R.T.Sauer (1995).
Minor groove DNA-recognition by alpha-helices.
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Homeotic genes and diversification of the insect body plan.
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YY1 facilitates the association of serum response factor with the c-fos serum response element.
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The optimal binding sequence of the Hox11 protein contains a predicted recognition core motif.
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From carpet bombing to cruise missiles: the 'second-order' mechanisms used by transcription factors to ensure specific DNA binding in vivo.
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Crystallization and preliminary X-ray diffraction studies of an a1/alpha 2/DNA ternary complex.
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Homeodomains: together again for the first time.
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7628011 W.Yang, and T.A.Steitz (1995).
Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site.
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PDB code: 1gdt
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The Drosophila tissue-specific factor Grainyhead contains novel DNA-binding and dimerization domains which are conserved in the human protein CP2.
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An altered-specificity mutation in a human POU domain demonstrates functional analogy between the POU-specific subdomain and phage lambda repressor.
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Sequence-specific DNA recognition by Cys2, His2 zinc fingers.
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The Drosophila sine oculis locus encodes a homeodomain-containing protein required for the development of the entire visual system.
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Recognition of a DNA operator by a dimer composed of two different homeodomain proteins.