PDBsum entry 1yrn

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protein dna_rna Protein-protein interface(s) links
DNA binding protein/DNA PDB id
Protein chains
49 a.a. *
78 a.a. *
Waters ×58
* Residue conservation analysis
PDB id:
Name: DNA binding protein/DNA
Title: Crystal structure of the mata1/matalpha2 homeodomain heterodimer bound to DNA
Structure: DNA (5'- d( Tp Ap Cp Ap Tp Gp Tp Ap Ap Tp Tp Tp Ap Tp Tp Ap C p Ap Tp Cp A)-3'). Chain: c. Engineered: yes. DNA (5'- d( Tp Ap Tp Gp Ap Tp Gp Tp Ap Ap Tp Ap Ap Ap Tp Tp A p Cp Ap Tp G)-3'). Chain: d.
Source: Synthetic: yes. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: mat a1 residue 66-126. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: t7 promoter. Gene: mat alpha2 residue 128-210.
Biol. unit: Dimer (from PQS)
2.50Å     R-factor:   0.225     R-free:   0.298
Authors: T.Li,M.R.Stark,A.D.Johnson,C.Wolberger
Key ref: T.Li et al. (1995). Crystal structure of the MATa1/MAT alpha 2 homeodomain heterodimer bound to DNA. Science, 270, 262-269. PubMed id: 7569974 DOI: 10.1126/science.270.5234.262
02-Nov-95     Release date:   29-Jan-96    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P0CY10  (MATA1_YEASX) -  Mating-type protein A1
126 a.a.
49 a.a.
Protein chain
Pfam   ArchSchema ?
P0CY08  (MTAL2_YEAST) -  Mating-type protein ALPHA2
210 a.a.
78 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     DNA binding     2 terms  


DOI no: 10.1126/science.270.5234.262 Science 270:262-269 (1995)
PubMed id: 7569974  
Crystal structure of the MATa1/MAT alpha 2 homeodomain heterodimer bound to DNA.
T.Li, M.R.Stark, A.D.Johnson, C.Wolberger.
The Saccharomyces cerevisiae MATa1 and MAT alpha 2 homeodomain proteins, which play a role in determining yeast cell type, form a heterodimer that binds DNA and represses transcription in a cell type-specific manner. Whereas the alpha 2 and a1 proteins on their own have only modest affinity for DNA, the a1/alpha 2 heterodimer binds DNA with high specificity and affinity. The three-dimensional crystal structure of the a1/alpha 2 homeodomain heterodimer bound to DNA was determined at a resolution of 2.5 A. The a1 and alpha 2 homeodomains bind in a head-to-tail orientation, with heterodimer contacts mediated by a 16-residue tail located carboxyl-terminal to the alpha 2 homeodomain. This tail becomes ordered in the presence of a1, part of it forming a short amphipathic helix that packs against the a1 homeodomain between helices 1 and 2. A pronounced 60 degree bend is induced in the DNA, which makes possible protein-protein and protein-DNA contacts that could not take place in a straight DNA fragment. Complex formation mediated by flexible protein-recognition peptides attached to stably folded DNA binding domains may prove to be a general feature of the architecture of other classes of eukaryotic transcriptional regulators.

Literature references that cite this PDB file's key reference

  PubMed id Reference
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PDB codes: 3a01 3a02 3a03 3lnq
19486297 B.C.Stanton, S.S.Giles, E.K.Kruzel, C.L.Warren, A.Z.Ansari, and C.M.Hull (2009).
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Functional specificity of a Hox protein mediated by the recognition of minor groove structure.
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PDB codes: 2r5y 2r5z
18059448 S.C.Harrison (2007).
Three-dimensional intricacies in protein-DNA recognition and transcriptional control.
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PDB code: 2hzd
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Decoding transcriptional regulatory interactions.
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15869395 A.Sarai, and H.Kono (2005).
Protein-DNA recognition patterns and predictions.
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15634343 M.F.Tioni, I.L.Viola, R.L.Chan, and D.H.Gonzalez (2005).
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Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites.
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15853794 Y.Chen, and G.Varani (2005).
Protein families and RNA recognition.
  FEBS J, 272, 2088-2097.  
15247345 M.D.Simon, K.Sato, G.A.Weiss, and K.M.Shokat (2004).
A phage display selection of engrailed homeodomain mutants and the importance of residue Q50.
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15388867 R.Schleif, and C.Wolberger (2004).
Arm-domain interactions can provide high binding cooperativity.
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15331021 V.H.Nagaraj, R.A.O'Flanagan, A.R.Bruning, J.R.Mathias, A.K.Vershon, and A.M.Sengupta (2004).
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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
12612071 I.Saadi, A.Kuburas, J.J.Engle, and A.F.Russo (2003).
Dominant negative dimerization of a mutant homeodomain protein in Axenfeld-Rieger syndrome.
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12784213 J.Aishima, and C.Wolberger (2003).
Insights into nonspecific binding of homeodomains from a structure of MATalpha2 bound to DNA.
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14580198 K.J.Hwang, B.Xiang, J.M.Gruschus, K.Y.Nam, K.T.No, M.Nirenberg, and J.A.Ferretti (2003).
Distortion of the three-dimensional structure of the vnd/NK-2 homeodomain bound to DNA induced by an embryonically lethal A35T point mutation.
  Biochemistry, 42, 12522-12531.
PDB code: 1qry
12684382 T.Srikantha, S.A.Lachke, and D.R.Soll (2003).
Three mating type-like loci in Candida glabrata.
  Eukaryot Cell, 2, 328-340.  
12121651 A.Ke, J.R.Mathias, A.K.Vershon, and C.Wolberger (2002).
Structural and thermodynamic characterization of the DNA binding properties of a triple alanine mutant of MATalpha2.
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PDB code: 1le8
12464634 C.M.Hull, R.C.Davidson, and J.Heitman (2002).
Cell identity and sexual development in Cryptococcus neoformans are controlled by the mating-type-specific homeodomain protein Sxi1alpha.
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A Hoogsteen base pair embedded in undistorted B-DNA.
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PDB code: 1k61
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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
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
11861910 Z.Morávek, S.Neidle, and B.Schneider (2002).
Protein and drug interactions in the minor groove of DNA.
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11741530 C.W.Garvie, and C.Wolberger (2001).
Recognition of specific DNA sequences.
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11779502 C.W.Garvie, J.Hagman, and C.Wolberger (2001).
Structural studies of Ets-1/Pax5 complex formation on DNA.
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PDB codes: 1k78 1k79 1k7a
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Nuclear-receptor interactions on DNA-response elements.
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PDB code: 1hlv
10856250 E.Gillitzer, G.Chen, and A.Stenlund (2000).
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10627562 G.Chen, and A.Stenlund (2000).
Two patches of amino acids on the E2 DNA binding domain define the surface for interaction with E1.
  J Virol, 74, 1506-1512.  
10940257 L.D.Williams, and L.J.Maher (2000).
Electrostatic mechanisms of DNA deformation.
  Annu Rev Biophys Biomol Struct, 29, 497-521.  
10733977 L.Pardo, M.Campillo, D.Bosch, N.Pastor, and H.Weinstein (2000).
Binding mechanisms of TATA box-binding proteins: DNA kinking is stabilized by specific hydrogen bonds.
  Biophys J, 78, 1988-1996.  
10759558 R.L.Smith, and A.D.Johnson (2000).
A sequence resembling a peroxisomal targeting sequence directs the interaction between the tetratricopeptide repeats of Ssn6 and the homeodomain of alpha 2.
  Proc Natl Acad Sci U S A, 97, 3901-3906.  
10629049 S.S.Mahajan, and A.C.Wilson (2000).
Mutations in host cell factor 1 separate its role in cell proliferation from recruitment of VP16 and LZIP.
  Mol Cell Biol, 20, 919-928.  
10931305 T.Romeis, A.Brachmann, R.Kahmann, and J.Kämper (2000).
Identification of a target gene for the bE-bW homeodomain protein complex in Ustilago maydis.
  Mol Microbiol, 37, 54-66.  
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.  
10813836 V.Nanda, and L.Brand (2000).
Aromatic interactions in homeodomains contribute to the low quantum yield of a conserved, buried tryptophan.
  Proteins, 40, 112-125.  
  10567520 A.Ravindra, K.Weiss, and R.T.Simpson (1999).
High-resolution structural analysis of chromatin at specific loci: Saccharomyces cerevisiae silent mating-type locus HMRa.
  Mol Cell Biol, 19, 7944-7950.  
10449733 B.S.Wang, and C.O.Pabo (1999).
Dimerization of zinc fingers mediated by peptides evolved in vitro from random sequences.
  Proc Natl Acad Sci U S A, 96, 9568-9573.  
10410794 C.Wolberger (1999).
Multiprotein-DNA complexes in transcriptional regulation.
  Annu Rev Biophys Biomol Struct, 28, 29-56.  
10541551 D.Chasman, K.Cepek, P.A.Sharp, and C.O.Pabo (1999).
Crystal structure of an OCA-B peptide bound to an Oct-1 POU domain/octamer DNA complex: specific recognition of a protein-DNA interface.
  Genes Dev, 13, 2650-2657.
PDB code: 1cqt
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
10090291 H.Kono, and A.Sarai (1999).
Structure-based prediction of DNA target sites by regulatory proteins.
  Proteins, 35, 114-131.  
  10082522 J.J.Tremblay, and J.Drouin (1999).
Egr-1 is a downstream effector of GnRH and synergizes by direct interaction with Ptx1 and SF-1 to enhance luteinizing hormone beta gene transcription.
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10026283 K.Nadassy, S.J.Wodak, and J.Janin (1999).
Structural features of protein-nucleic acid recognition sites.
  Biochemistry, 38, 1999-2017.  
10047576 L.Chen (1999).
Combinatorial gene regulation by eukaryotic transcription factors.
  Curr Opin Struct Biol, 9, 48-55.  
10541438 M.L.Tejada, Z.Jia, D.May, and R.G.Deeley (1999).
Determinants of the DNA-binding specificity of the Avian homeodomain protein, AKR.
  DNA Cell Biol, 18, 791-804.  
10075932 M.R.Stark, D.Escher, and A.D.Johnson (1999).
A trans-acting peptide activates the yeast a1 repressor by raising its DNA-binding affinity.
  EMBO J, 18, 1621-1629.  
10336376 R.Schleif (1999).
Arm-domain interactions in proteins: a review.
  Proteins, 34, 1-3.  
10375516 S.Khorasanizadeh, and F.Rastinejad (1999).
Transcription factors: the right combination for the DNA lock.
  Curr Biol, 9, R456-R458.  
  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.  
  10398682 Y.Liu, W.Gong, C.C.Huang, W.Herr, and X.Cheng (1999).
Crystal structure of the conserved core of the herpes simplex virus transcriptional regulatory protein VP16.
  Genes Dev, 13, 1692-1703.
PDB code: 16vp
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.  
9794820 C.Wolberger (1998).
Combinatorial transcription factors.
  Curr Opin Genet Dev, 8, 552-559.  
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.
  EMBO J, 17, 7404-7415.
PDB codes: 1b01 2cpg
9922128 J.C.Hansen, C.Tse, and A.P.Wolffe (1998).
Structure and function of the core histone N-termini: more than meets the eye.
  Biochemistry, 37, 17637-17641.  
9928492 J.E.Haber (1998).
Mating-type gene switching in Saccharomyces cerevisiae.
  Annu Rev Genet, 32, 561-599.  
9691271 J.K.Strauss-Soukup, P.D.Rodrigues, and L.J.Maher (1998).
Effect of base composition on DNA bending by phosphate neutralization.
  Biophys Chem, 72, 297-306.  
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.  
  9529887 L.A.Casselton, and N.S.Olesnicky (1998).
Molecular genetics of mating recognition in basidiomycete fungi.
  Microbiol Mol Biol Rev, 62, 55-70.  
9580678 L.A.Tomky, J.K.Strauss-Soukup, and L.J.Maher (1998).
Effects of phosphate neutralization on the shape of the AP-1 transcription factor binding site in duplex DNA.
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10384309 M.Wahi, K.Komachi, and A.D.Johnson (1998).
Gene regulation by the yeast Ssn6-Tup1 corepressor.
  Cold Spring Harb Symp Quant Biol, 63, 447-457.  
9695950 P.R.Johnson, R.Swanson, L.Rakhilina, and M.Hochstrasser (1998).
Degradation signal masking by heterodimerization of MATalpha2 and MATa1 blocks their mutual destruction by the ubiquitin-proteasome pathway.
  Cell, 94, 217-227.  
9518483 R.E.Dickerson (1998).
DNA bending: the prevalence of kinkiness and the virtues of normality.
  Nucleic Acids Res, 26, 1906-1926.  
9699631 S.A.Dames, R.A.Kammerer, R.Wiltscheck, J.Engel, and A.T.Alexandrescu (1998).
NMR structure of a parallel homotrimeric coiled coil.
  Nat Struct Biol, 5, 687-691.
PDB code: 1aq5
9519295 S.Tan, and T.J.Richmond (1998).
Eukaryotic transcription factors.
  Curr Opin Struct Biol, 8, 41-48.  
9864368 V.Kurvari, N.V.Grishin, and W.J.Snell (1998).
A gamete-specific, sex-limited homeodomain protein in Chlamydomonas.
  J Cell Biol, 143, 1971-1980.  
10384325 W.Herr (1998).
The herpes simplex virus VP16-induced complex: mechanisms of combinatorial transcriptional regulation.
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9254598 D.N.Paolella, Y.Liu, M.A.Fabian, and A.Schepartz (1997).
Electrostatic mechanism for DNA bending by bZIP proteins.
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Eukaryotic transcription factor-DNA complexes.
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Linker length and composition influence the flexibility of Oct-1 DNA binding.
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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.
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9012668 J.H.Carra, and P.L.Privalov (1997).
Energetics of folding and DNA binding of the MAT alpha 2 homeodomain.
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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
  9199328 J.S.Lai, and W.Herr (1997).
Interdigitated residues within a small region of VP16 interact with Oct-1, HCF, and DNA.
  Mol Cell Biol, 17, 3937-3946.  
9188697 L.Li, and K.S.Matthews (1997).
Differences in water release with DNA binding by ultrabithorax and deformed homeodomains.
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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.
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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.  
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Conformational changes induced in Hoxb-8/Pbx-1 heterodimers in solution and upon interaction with specific DNA.
  Mol Cell Biol, 17, 5369-5376.  
9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
  Biopolymers, 44, 361-403.  
9405381 S.Schumacher, R.T.Clubb, M.Cai, K.Mizuuchi, G.M.Clore, and A.M.Gronenborn (1997).
Solution structure of the Mu end DNA-binding ibeta subdomain of phage Mu transposase: modular DNA recognition by two tethered domains.
  EMBO J, 16, 7532-7541.
PDB codes: 2ezk 2ezl
9047333 T.Akiyama, and M.E.Hogan (1997).
Structural analysis of DNA bending induced by tethered triple helix forming oligonucleotides.
  Biochemistry, 36, 2307-2315.  
9184234 T.K.Kerppola, and T.Curran (1997).
The transcription activation domains of Fos and Jun induce DNA bending through electrostatic interactions.
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Schizophyllum commune A alpha mating-type proteins, Y and Z, form complexes in all combinations in vitro.
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9171356 Y.Ling, J.H.Lakey, C.E.Roberts, and A.D.Sharrocks (1997).
Molecular characterization of the B-box protein-protein interaction motif of the ETS-domain transcription factor Elk-1.
  EMBO J, 16, 2431-2440.  
8989317 Y.Xing, D.Guha Thakurta, and D.E.Draper (1997).
The RNA binding domain of ribosomal protein L11 is structurally similar to homeodomains.
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8768896 A.K.Vershon (1996).
Protein interactions of homeodomain proteins.
  Curr Opin Biotechnol, 7, 392-396.  
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Homeodomain interactions.
  Curr Opin Struct Biol, 6, 62-68.  
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Conservation and diversification in homeodomain-DNA interactions: a comparative genetic analysis.
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  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.  
8807901 J.K.Strauss, T.P.Prakash, C.Roberts, C.Switzer, and L.J.Maher (1996).
DNA bending by a phantom protein.
  Chem Biol, 3, 671-678.  
  8628280 J.Mead, H.Zhong, T.B.Acton, and A.K.Vershon (1996).
The yeast alpha2 and Mcm1 proteins interact through a region similar to a motif found in homeodomain proteins of higher eukaryotes.
  Mol Cell Biol, 16, 2135-2143.  
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.  
  8698039 L.T.Peltenburg, and C.Murre (1996).
Engrailed and Hox homeodomain proteins contain a related Pbx interaction motif that recognizes a common structure present in Pbx.
  EMBO J, 15, 3385-3393.  
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.  
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.  
8612267 R.Kahmann, and M.Bölker (1996).
Self/nonself recognition in fungi: old mysteries and simple solutions.
  Cell, 85, 145-148.  
8763497 R.S.Mann, and S.K.Chan (1996).
Extra specificity from extradenticle: the partnership between HOX and PBX/EXD homeodomain proteins.
  Trends Genet, 12, 258-262.  
15157513 S.J.Hiscock, U.Kües, and H.G.Dickinson (1996).
Molecular mechanisms of self-incompatibility in flowering plants and fungi - different means to the same end.
  Trends Cell Biol, 6, 421-428.  
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.
  Proc Natl Acad Sci U S A, 93, 5223-5228.  
8901543 T.Akiyama, and M.E.Hogan (1996).
The design of an agent to bend DNA.
  Proc Natl Acad Sci U S A, 93, 12122-12127.  
  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.
  EMBO J, 15, 4981-4991.  
8591025 T.Tullius (1995).
Homeodomains: together again for the first time.
  Structure, 3, 1143-1145.  
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