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Gene regulation/DNA PDB id
1pdn
Jmol
Contents
Protein chain
123 a.a. *
DNA/RNA
Waters ×13
* Residue conservation analysis
PDB id:
1pdn
Name: Gene regulation/DNA
Title: Crystal structure of a paired domain-DNA complex at 2.5 angstroms resolution reveals structural basis for pax developmental mutations
Structure: DNA (5'- d( Ap Ap Cp Gp Tp Cp Ap Cp Gp Gp Tp Tp Gp Ap C)-3'). Chain: a. Engineered: yes. DNA (5'- d( Tp Tp Gp Tp Cp Ap Ap Cp Cp Gp Tp Gp Ap Cp G)-3'). Chain: b. Engineered: yes. Protein (prd paired).
Source: Synthetic: yes. Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: prd. Expressed in: bl21(de3).
Biol. unit: Trimer (from PQS)
Resolution:
2.50Å     R-factor:   0.234     R-free:   0.284
Authors: W.Xu,M.A.Rould,S.Jun,C.Desplan,C.O.Pabo
Key ref: W.Xu et al. (1995). Crystal structure of a paired domain-DNA complex at 2.5 A resolution reveals structural basis for Pax developmental mutations. Cell, 80, 639-650. PubMed id: 7867071 DOI: 10.1016/0092-8674(95)90518-9
Date:
16-May-95     Release date:   31-Jul-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06601  (PRD_DROME) -  Segmentation protein paired
Seq:
Struc: 		 
Seq:
Struc: 		613 a.a.
123 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

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

 

 
DOI no: 10.1016/0092-8674(95)90518-9 Cell 80:639-650 (1995)
PubMed id: 7867071  
 
 
Crystal structure of a paired domain-DNA complex at 2.5 A resolution reveals structural basis for Pax developmental mutations.
W.Xu, M.A.Rould, S.Jun, C.Desplan, C.O.Pabo.
 
  ABSTRACT  
 
The 2.5 A resolution structure of a cocrystal containing the paired domain from the Drosophila paired (prd) protein and a 15 bp site shows structurally independent N-terminal and C-terminal subdomains. Each of these domains contains a helical region resembling the homeodomain and the Hin recombinase. The N-terminal domain makes extensive DNA contacts, using a novel beta turn motif that binds in the minor groove and a helix-turn-helix unit with a docking arrangement surprisingly similar to that of the lambda repressor. The C-terminal domain is not essential for prd binding and does not contact the optimized site. All known developmental missense mutations in the paired box of mammalian Pax genes map to the N-terminal subdomain, and most of them are found at the protein-DNA interface.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20943750 S.H.Cross, L.McKie, K.West, E.L.Coghill, J.Favor, S.Bhattacharya, S.D.Brown, and I.J.Jackson (2011).
The Opdc missense mutation of Pax2 has a milder than loss-of-function phenotype.
  Hum Mol Genet, 20, 223-234.  
  20664694 F.Cai, J.Zhu, W.Chen, T.Ke, F.Wang, X.Tu, Y.Zhang, R.Jin, and X.Wu (2010).
A novel PAX6 mutation in a large Chinese family with aniridia and congenital cataract.
  Mol Vis, 16, 1141-1145.  
20132240 H.Kokotas, and M.B.Petersen (2010).
Clinical and molecular aspects of aniridia.
  Clin Genet, 77, 409-420.  
20221250 R.P.Alur, C.Vijayasarathy, J.D.Brown, M.Mehtani, I.F.Onojafe, Y.V.Sergeev, E.Boobalan, M.Jones, K.Tang, H.Liu, C.H.Xia, X.Gong, and B.P.Brooks (2010).
Papillorenal syndrome-causing missense mutations in PAX2/Pax2 result in hypomorphic alleles in mouse and human.
  PLoS Genet, 6, e1000870.  
20718765 T.Di Palma, E.Zampella, M.G.Filippone, P.E.Macchia, C.Ris-Stalpers, M.de Vroede, and M.Zannini (2010).
Characterization of a novel loss-of-function mutation of PAX8 associated with congenital hypothyroidism.
  Clin Endocrinol (Oxf), 73, 808-814.  
20127975 V.Pingault, D.Ente, F.Dastot-Le Moal, M.Goossens, S.Marlin, and N.Bondurand (2010).
Review and update of mutations causing Waardenburg syndrome.
  Hum Mutat, 31, 391-406.  
19406113 B.M.Weasner, B.Weasner, S.M.Deyoung, S.D.Michaels, and J.P.Kumar (2009).
Transcriptional activities of the Pax6 gene eyeless regulate tissue specificity of ectopic eye formation in Drosophila.
  Dev Biol, 334, 492-502.  
  19794903 G.R.Dressler (2009).
The specification and maintenance of renal cell types by epigenetic factors.
  Organogenesis, 5, 73-82.  
19666017 J.Clements, K.Hens, S.Merugu, B.Dichtl, H.G.de Couet, and P.Callaerts (2009).
Mutational analysis of the eyeless gene and phenotypic rescue reveal that an intact Eyeless protein is necessary for normal eye and brain development in Drosophila.
  Dev Biol, 334, 503-512.  
18983540 J.D.Kubic, K.P.Young, R.S.Plummer, A.E.Ludvik, and D.Lang (2008).
Pigmentation PAX-ways: the role of Pax3 in melanogenesis, melanocyte stem cell maintenance, and disease.
  Pigment Cell Melanoma Res, 21, 627-645.  
18829450 L.Codutti, H.van Ingen, C.Vascotto, F.Fogolari, A.Corazza, G.Tell, F.Quadrifoglio, P.Viglino, R.Boelens, and G.Esposito (2008).
The Solution Structure of DNA-free Pax-8 Paired Box Domain Accounts for Redox Regulation of Transcriptional Activity in the Pax Protein Family.
  J Biol Chem, 283, 33321-33328.
PDB code: 2k27
17998914 M.L.Holmes, C.Pridans, and S.L.Nutt (2008).
The regulation of the B-cell gene expression programme by Pax5.
  Immunol Cell Biol, 86, 47-53.  
18655061 N.Andrusier, E.Mashiach, R.Nussinov, and H.J.Wolfson (2008).
Principles of flexible protein-protein docking.
  Proteins, 73, 271-289.  
17980011 S.A.Esperante, C.M.Rivolta, L.Miravalle, V.Herzovich, S.Iorcansky, M.Baralle, and H.M.Targovnik (2008).
Identification and characterization of four PAX8 rare sequence variants (p.T225M, p.L233L, p.G336S and p.A439A) in patients with congenital hypothyroidism and dysgenetic thyroid glands.
  Clin Endocrinol (Oxf), 68, 828-835.  
18473110 S.Short, and L.Z.Holland (2008).
The evolution of alternative splicing in the Pax family: the view from the Basal chordate amphioxus.
  J Mol Evol, 66, 605-620.  
  17417613 A.Dansault, G.David, C.Schwartz, C.Jaliffa, V.Vieira, G.de la Houssaye, K.Bigot, F.Catin, L.Tattu, C.Chopin, P.Halimi, O.Roche, N.Van Regemorter, F.Munier, D.Schorderet, J.L.Dufier, C.Marsac, D.Ricquier, M.Menasche, A.Penfornis, and M.Abitbol (2007).
Three new PAX6 mutations including one causing an unusual ophthalmic phenotype associated with neurodevelopmental abnormalities.
  Mol Vis, 13, 511-523.  
17910065 J.Zhao, Q.Hu, Y.Chen, S.Luo, L.Bao, and Y.Xu (2007).
A novel missense mutation in the paired domain of human PAX9 causes oligodontia.
  Am J Med Genet A, 143, 2592-2597.  
17437516 M.Tonacchera, M.E.Banco, L.Montanelli, C.Di Cosmo, P.Agretti, G.De Marco, E.Ferrarini, A.Ordookhani, A.Perri, L.Chiovato, F.Santini, P.Vitti, and A.Pinchera (2007).
Genetic analysis of the PAX8 gene in children with congenital hypothyroidism and dysgenetic or eutopic thyroid glands: identification of a novel sequence variant.
  Clin Endocrinol (Oxf), 67, 34-40.  
16479262 H.Kapadia, S.Frazier-Bowers, T.Ogawa, and R.N.D'Souza (2006).
Molecular characterization of a novel PAX9 missense mutation causing posterior tooth agenesis.
  Eur J Hum Genet, 14, 403-409.  
16585527 T.V.Pereira, F.M.Salzano, A.Mostowska, W.H.Trzeciak, A.Ruiz-Linares, J.A.Chies, C.Saavedra, C.Nagamachi, A.M.Hurtado, K.Hill, D.Castro-de-Guerra, W.A.Silva-Júnior, and M.C.Bortolini (2006).
Natural selection and molecular evolution in primate PAX9 gene, a major determinant of tooth development.
  Proc Natl Acad Sci U S A, 103, 5676-5681.  
15831788 C.Feschotte, M.T.Osterlund, R.Peeler, and S.R.Wessler (2005).
DNA-binding specificity of rice mariner-like transposases and interactions with Stowaway MITEs.
  Nucleic Acids Res, 33, 2153-2165.  
15702348 J.C.Brownlie, N.M.Johnson, and S.Whyard (2005).
The Caenorhabditis briggsae genome contains active CbmaT1 and Tcb1 transposons.
  Mol Genet Genomics, 273, 92.  
15772827 R.B.White, T.M.Lamey, M.Ziman, and A.Koenders (2005).
Isolation and expression analysis of a Pax group III gene from the crustacean Cherax destructor.
  Dev Genes Evol, 215, 306-312.  
15688409 S.Du, E.J.Lawrence, D.Strzelecki, P.Rajput, S.J.Xia, D.M.Gottesman, and F.G.Barr (2005).
Co-expression of alternatively spliced forms of PAX3, PAX7, PAX3-FKHR and PAX7-FKHR with distinct DNA binding and transactivation properties in rhabdomyosarcoma.
  Int J Cancer, 115, 85-92.  
15888455 X.Cao, F.Kambe, X.Lu, N.Kobayashi, S.Ohmori, and H.Seo (2005).
Glutathionylation of two cysteine residues in paired domain regulates DNA binding activity of Pax-8.
  J Biol Chem, 280, 25901-25906.  
15950457 Z.Kozmik (2005).
Pax genes in eye development and evolution.
  Curr Opin Genet Dev, 15, 430-438.  
15579687 H.N.Cinar, and A.D.Chisholm (2004).
Genetic analysis of the Caenorhabditis elegans pax-6 locus: roles of paired domain-containing and nonpaired domain-containing isoforms.
  Genetics, 168, 1307-1322.  
14607846 J.K.Mensah, T.Ogawa, H.Kapadia, A.C.Cavender, and R.N.D'Souza (2004).
Functional analysis of a mutation in PAX9 associated with familial tooth agenesis in humans.
  J Biol Chem, 279, 5924-5933.  
15148315 S.Apuzzo, A.Abdelhakim, A.S.Fortin, and P.Gros (2004).
Cross-talk between the paired domain and the homeodomain of Pax3: DNA binding by each domain causes a structural change in the other domain, supporting interdependence for DNA Binding.
  J Biol Chem, 279, 33601-33612.  
15304566 S.Watkins, G.van Pouderoyen, and T.K.Sixma (2004).
Structural analysis of the bipartite DNA-binding domain of Tc3 transposase bound to transposon DNA.
  Nucleic Acids Res, 32, 4306-4312.
PDB code: 1u78
12833550 B.D.Paul, A.Kanhere, A.Chakraborty, M.Bansal, and V.Nagaraja (2003).
Identification of the domains for DNA binding and transactivation function of C protein from bacteriophage Mu.
  Proteins, 52, 272-282.  
12670990 J.Ashour, and M.K.Hondalus (2003).
Phenotypic mutants of the intracellular actinomycete Rhodococcus equi created by in vivo Himar1 transposon mutagenesis.
  J Bacteriol, 185, 2644-2652.  
14515373 K.Bastard, A.Thureau, R.Lavery, and C.Prévost (2003).
Docking macromolecules with flexible segments.
  J Comput Chem, 24, 1910-1920.  
12552561 L.Y.Chao, R.Mishra, L.C.Strong, and G.F.Saunders (2003).
Missense mutations in the DNA-binding region and termination codon in PAX6.
  Hum Mutat, 21, 138-145.  
12692125 M.Ganga, H.M.Espinoza, C.J.Cox, L.Morton, T.A.Hjalt, Y.Lee, and B.A.Amendt (2003).
PITX2 isoform-specific regulation of atrial natriuretic factor expression: synergism and repression with Nkx2.5.
  J Biol Chem, 278, 22437-22445.  
  12100888 F.Pichaud, and C.Desplan (2002).
Pax genes and eye organogenesis.
  Curr Opin Genet Dev, 12, 430-434.  
  11750700 N.Chi, and J.A.Epstein (2002).
Getting your Pax straight: Pax proteins in development and disease.
  Trends Genet, 18, 41-47.  
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.
  J Biol Chem, 277, 26200-26207.  
12388550 R.Mishra, I.P.Gorlov, L.Y.Chao, S.Singh, and G.F.Saunders (2002).
PAX6, paired domain influences sequence recognition by the homeodomain.
  J Biol Chem, 277, 49488-49494.  
12421758 Y.H.Zhou, J.B.Zheng, X.Gu, G.F.Saunders, and W.K.Yung (2002).
Novel PAX6 binding sites in the human genome and the role of repetitive elements in the evolution of gene regulation.
  Genome Res, 12, 1716-1722.  
12082109 Z.Izsvák, D.Khare, J.Behlke, U.Heinemann, R.H.Plasterk, and Z.Ivics (2002).
Involvement of a bifunctional, paired-like DNA-binding domain and a transpositional enhancer in Sleeping Beauty transposition.
  J Biol Chem, 277, 34581-34588.  
11861910 Z.Morávek, S.Neidle, and B.Schneider (2002).
Protein and drug interactions in the minor groove of DNA.
  Nucleic Acids Res, 30, 1182-1191.  
11779502 C.W.Garvie, J.Hagman, and C.Wolberger (2001).
Structural studies of Ets-1/Pax5 complex formation on DNA.
  Mol Cell, 8, 1267-1276.
PDB codes: 1k78 1k79 1k7a
11179888 C.W.Müller (2001).
Transcription factors: global and detailed views.
  Curr Opin Struct Biol, 11, 26-32.  
11600704 D.Fitzsimmons, R.Lutz, W.Wheat, H.M.Chamberlin, and J.Hagman (2001).
Highly conserved amino acids in Pax and Ets proteins are required for DNA binding and ternary complex assembly.
  Nucleic Acids Res, 29, 4154-4165.  
11698662 H.E.Xu, M.H.Lambert, V.G.Montana, K.D.Plunket, L.B.Moore, J.L.Collins, J.A.Oplinger, S.A.Kliewer, R.T.Gampe, D.D.McKee, J.T.Moore, and T.M.Willson (2001).
Structural determinants of ligand binding selectivity between the peroxisome proliferator-activated receptors.
  Proc Natl Acad Sci U S A, 98, 13919-13924.
PDB codes: 1k74 1k7l
  11103953 D.A.Underhill (2000).
Genetic and biochemical diversity in the Pax gene family.
  Biochem Cell Biol, 78, 629-638.  
10781047 D.J.Miller, D.C.Hayward, J.S.Reece-Hoyes, I.Scholten, J.Catmull, W.J.Gehring, P.Callaerts, J.E.Larsen, and E.E.Ball (2000).
Pax gene diversity in the basal cnidarian Acropora millepora (Cnidaria, Anthozoa): implications for the evolution of the Pax gene family.
  Proc Natl Acad Sci U S A, 97, 4475-4480.  
11032856 D.Lang, F.Chen, R.Milewski, J.Li, M.M.Lu, and J.A.Epstein (2000).
Pax3 is required for enteric ganglia formation and functions with Sox10 to modulate expression of c-ret.
  J Clin Invest, 106, 963-971.  
10737978 L.Y.Chao, V.Huff, L.C.Strong, and G.F.Saunders (2000).
Mutation in the PAX6 gene in twenty patients with aniridia.
  Hum Mutat, 15, 332-339.  
10908331 M.S.Lechner, I.Levitan, and G.R.Dressler (2000).
PTIP, a novel BRCT domain-containing protein interacts with Pax2 and is associated with active chromatin.
  Nucleic Acids Res, 28, 2741-2751.  
  11104519 N.M.Luscombe, S.E.Austin, H.M.Berman, and J.M.Thornton (2000).
An overview of the structures of protein-DNA complexes.
  Genome Biol, 1, REVIEWS001.  
10613862 P.Manna, R.P.Nieder, and M.R.Schaefer (2000).
DNA-Binding properties of the Fremyella diplosiphon RpbA repressor.
  J Bacteriol, 182, 51-56.  
10393185 A.D.Hollenbach, J.E.Sublett, C.J.McPherson, and G.Grosveld (1999).
The Pax3-FKHR oncoprotein is unresponsive to the Pax3-associated repressor hDaxx.
  EMBO J, 18, 3702-3711.  
9892673 B.Hauck, W.J.Gehring, and U.Walldorf (1999).
Functional analysis of an eye specific enhancer of the eyeless gene in Drosophila.
  Proc Natl Acad Sci U S A, 96, 564-569.  
  10074170 F.M.van den Ent, A.Vos, and R.H.Plasterk (1999).
Dissecting the role of the N-terminal domain of human immunodeficiency virus integrase by trans-complementation analysis.
  J Virol, 73, 3176-3183.  
  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
10090291 H.Kono, and A.Sarai (1999).
Structure-based prediction of DNA target sites by regulatory proteins.
  Proteins, 35, 114-131.  
  10511553 H.M.Chamberlin, K.B.Brown, P.W.Sternberg, and J.H.Thomas (1999).
Characterization of seven genes affecting Caenorhabditis elegans hindgut development.
  Genetics, 153, 731-742.  
10329718 I.Mikkola, J.A.Bruun, G.Bjorkoy, T.Holm, and T.Johansen (1999).
Phosphorylation of the transactivation domain of Pax6 by extracellular signal-regulated kinase and p38 mitogen-activated protein kinase.
  J Biol Chem, 274, 15115-15126.  
10026283 K.Nadassy, S.J.Wodak, and J.Janin (1999).
Structural features of protein-nucleic acid recognition sites.
  Biochemistry, 38, 1999-2017.  
10533062 L.A.Schimmenti, H.H.Shim, J.D.Wirtschafter, V.A.Panzarino, C.E.Kashtan, S.J.Kirkpatrick, D.S.Wargowski, T.D.France, E.Michel, and W.B.Dobyns (1999).
Homonucleotide expansion and contraction mutations of PAX2 and inclusion of Chiari 1 malformation as part of renal-coloboma syndrome.
  Hum Mutat, 14, 369-376.  
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.
  J Biol Chem, 274, 26894-26900.  
10466411 M.R.Eccles, and L.A.Schimmenti (1999).
Renal-coloboma syndrome: a multi-system developmental disorder caused by PAX2 mutations.
  Clin Genet, 56, 1-9.  
10441571 N.Azuma, Y.Yamaguchi, H.Handa, M.Hayakawa, A.Kanai, and M.Yamada (1999).
Missense mutation in the alternative splice region of the PAX6 gene in eye anomalies.
  Am J Hum Genet, 65, 656-663.  
  10354580 O.Hobert, and G.Ruvkun (1999).
Pax genes in Caenorhabditis elegans: a new twist.
  Trends Genet, 15, 214-216.  
  9858583 P.Y.Lam, J.E.Sublett, A.D.Hollenbach, and M.F.Roussel (1999).
The oncogenic potential of the Pax3-FKHR fusion protein requires the Pax3 homeodomain recognition helix but not the Pax3 paired-box DNA binding domain.
  Mol Cell Biol, 19, 594-601.  
  10431195 R.H.Plasterk, Z.Izsvák, and Z.Ivics (1999).
Resident aliens: the Tc1/mariner superfamily of transposable elements.
  Trends Genet, 15, 326-332.  
  10567552 S.B.Smith, H.C.Ee, J.R.Conners, and M.S.German (1999).
Paired-homeodomain transcription factor PAX4 acts as a transcriptional repressor in early pancreatic development.
  Mol Cell Biol, 19, 8272-8280.  
10430025 S.L.Nutt, and M.Busslinger (1999).
Monoallelic expression of Pax5: a paradigm for the haploinsufficiency of mammalian Pax genes?
  Biol Chem, 380, 601-611.  
10198632 T.Czerny, G.Halder, U.Kloter, A.Souabni, W.J.Gehring, and M.Busslinger (1999).
twin of eyeless, a second Pax-6 gene of Drosophila, acts upstream of eyeless in the control of eye development.
  Mol Cell, 3, 297-307.  
  10022910 W.Wheat, D.Fitzsimmons, H.Lennox, S.R.Krautkramer, L.N.Gentile, L.P.McIntosh, and J.Hagman (1999).
The highly conserved beta-hairpin of the paired DNA-binding domain is required for assembly of Pax-Ets ternary complexes.
  Mol Cell Biol, 19, 2231-2241.  
9737963 G.Tell, A.Scaloni, L.Pellizzari, S.Formisano, C.Pucillo, and G.Damante (1998).
Redox potential controls the structure and DNA binding activity of the paired domain.
  J Biol Chem, 273, 25062-25072.  
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.  
9482572 J.Prosser, and V.van Heyningen (1998).
PAX6 mutations reviewed.
  Hum Mutat, 11, 93.  
9706689 L.Pick (1998).
Segmentation: painting stripes from flies to vertebrates.
  Dev Genet, 23, 1.  
9590296 P.E.Macchia, P.Lapi, H.Krude, M.T.Pirro, C.Missero, L.Chiovato, A.Souabni, M.Baserga, V.Tassi, A.Pinchera, G.Fenzi, A.Grüters, M.Busslinger, and R.Di Lauro (1998).
PAX8 mutations associated with congenital hypothyroidism caused by thyroid dysgenesis.
  Nat Genet, 19, 83-86.  
  9573250 R.A.Lutzke, and R.H.Plasterk (1998).
Structure-based mutational analysis of the C-terminal DNA-binding domain of human immunodeficiency virus type 1 integrase: critical residues for protein oligomerization and DNA binding.
  J Virol, 72, 4841-4848.  
  9528779 R.Sharon-Friling, J.Richardson, S.Sperbeck, D.Lee, M.Rauchman, R.Maas, A.Swaroop, and G.Wistow (1998).
Lens-specific gene recruitment of zeta-crystallin through Pax6, Nrl-Maf, and brain suppressor sites.
  Mol Cell Biol, 18, 2067-2076.  
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.
  Proc Natl Acad Sci U S A, 95, 13720-13725.  
9724717 S.Rhee, R.G.Martin, J.L.Rosner, and D.R.Davies (1998).
A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator.
  Proc Natl Acad Sci U S A, 95, 10413-10418.
PDB code: 1bl0
9689035 W.J.Dreyer (1998).
The area code hypothesis revisited: olfactory receptors and other related transmembrane receptors may function as the last digits in a cell surface code for assembling embryos.
  Proc Natl Acad Sci U S A, 95, 9072-9077.  
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.  
9368756 A.P.Eijkelenboom, F.M.van den Ent, A.Vos, J.F.Doreleijers, K.Hård, T.D.Tullius, R.H.Plasterk, R.Kaptein, and R.Boelens (1997).
The solution structure of the amino-terminal HHCC domain of HIV-2 integrase: a three-helix bundle stabilized by zinc.
  Curr Biol, 7, 739-746.
PDB code: 1aub
  9279758 A.P.Read, and V.E.Newton (1997).
Waardenburg syndrome.
  J Med Genet, 34, 656-665.  
9288908 A.Poleev, O.Okladnova, A.M.Musti, S.Schneider, B.Royer-Pokora, and D.Plachov (1997).
Determination of functional domains of the human transcription factor PAX8 responsible for its nuclear localization and transactivating potential.
  Eur J Biochem, 247, 860-869.  
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.  
9241431 C.Chothia, T.Hubbard, S.Brenner, H.Barns, and A.Murzin (1997).
Protein folds in the all-beta and all-alpha classes.
  Annu Rev Biophys Biomol Struct, 26, 597-627.  
9297966 E.Dahl, H.Koseki, and R.Balling (1997).
Pax genes and organogenesis.
  Bioessays, 19, 755-765.  
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
9067759 H.Soejima, M.Fujimoto, K.Tsukamoto, N.Matsumoto, K.I.Yoshiura, Y.Fukushima, Y.Jinno, and N.Niikawa (1997).
Three novel PAX3 mutations observed in patients with Waardenburg syndrome type 1.
  Hum Mutat, 9, 177-180.  
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.  
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
9056723 P.Callaerts, G.Halder, and W.J.Gehring (1997).
PAX-6 in development and evolution.
  Annu Rev Neurosci, 20, 483-532.  
9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
  Biopolymers, 44, 361-403.  
9395405 Y.Tateno, K.Ikeo, T.Imanishi, H.Watanabe, T.Endo, Y.Yamaguchi, Y.Suzuki, K.Takahashi, K.Tsunoyama, M.Kawai, Y.Kawanishi, K.Naitou, and T.Gojobori (1997).
Evolutionary motif and its biological and structural significance.
  J Mol Evol, 44, S38-S43.  
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.  
9362493 Z.Kozmik, T.Czerny, and M.Busslinger (1997).
Alternatively spliced insertions in the paired domain restrict the DNA sequence specificity of Pax6 and Pax8.
  EMBO J, 16, 6793-6803.  
8760335 A.Cvekl, and J.Piatigorsky (1996).
Lens development and crystallin gene expression: many roles for Pax-6.
  Bioessays, 18, 621-630.  
  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.  
8696974 C.Wolberger (1996).
Homeodomain interactions.
  Curr Opin Struct Biol, 6, 62-68.  
8626478 D.E.Phelps, and G.R.Dressler (1996).
Identification of novel Pax-2 binding sites by chromatin precipitation.
  J Biol Chem, 271, 7978-7985.  
  8791518 D.Engelkamp, and V.van Heyningen (1996).
Transcription factors in disease.
  Curr Opin Genet Dev, 6, 334-342.  
8861910 E.Spanopoulou, F.Zaitseva, F.H.Wang, S.Santagata, D.Baltimore, and G.Panayotou (1996).
The homeodomain region of Rag-1 reveals the parallel mechanisms of bacterial and V(D)J recombination.
  Cell, 87, 263-276.  
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.  
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
8780507 I.Baikalov, I.Schröder, M.Kaczor-Grzeskowiak, K.Grzeskowiak, R.P.Gunsalus, and R.E.Dickerson (1996).
Structure of the Escherichia coli response regulator NarL.
  Biochemistry, 35, 11053-11061.
PDB code: 1rnl
8633043 J.A.Epstein, D.N.Shapiro, J.Cheng, P.Y.Lam, and R.L.Maas (1996).
Pax3 modulates expression of the c-Met receptor during limb muscle development.
  Proc Natl Acad Sci U S A, 93, 4213-4218.  
8943028 J.Favor, R.Sandulache, A.Neuhäuser-Klaus, W.Pretsch, B.Chatterjee, E.Senft, W.Wurst, V.Blanquet, P.Grimes, R.Spörle, and K.Schughart (1996).
The mouse Pax2(1Neu) mutation is identical to a human PAX2 mutation in a family with renal-coloboma syndrome and results in developmental defects of the brain, ear, eye, and kidney.
  Proc Natl Acad Sci U S A, 93, 13870-13875.  
  8552101 K.A.Koch, and D.J.Thiele (1996).
Autoactivation by a Candida glabrata copper metalloregulatory transcription factor requires critical minor groove interactions.
  Mol Cell Biol, 16, 724-734.  
  8943322 K.J.Vogan, D.A.Underhill, and P.Gros (1996).
An alternative splicing event in the Pax-3 paired domain identifies the linker region as a key determinant of paired domain DNA-binding activity.
  Mol Cell Biol, 16, 6677-6686.  
8640214 N.Azuma, S.Nishina, H.Yanagisawa, T.Okuyama, and M.Yamada (1996).
PAX6 missense mutation in isolated foveal hypoplasia.
  Nat Genet, 13, 141-142.  
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
8900176 S.Nornes, I.Mikkola, S.Krauss, M.Delghandi, M.Perander, and T.Johansen (1996).
Zebrafish Pax9 encodes two proteins with distinct C-terminal transactivating domains of different potency negatively regulated by adjacent N-terminal sequences.
  J Biol Chem, 271, 26914-26923.  
8643520 Z.Ivics, Z.Izsvak, A.Minter, and P.B.Hackett (1996).
Identification of functional domains and evolution of Tc1-like transposable elements.
  Proc Natl Acad Sci U S A, 93, 5008-5013.  
  7588606 A.Kispert, B.Koschorz, and B.G.Herrmann (1995).
The T protein encoded by Brachyury is a tissue-specific transcription factor.
  EMBO J, 14, 4763-4772.  
7795631 A.P.Read (1995).
Pax genes--paired feet in three camps.
  Nat Genet, 9, 333-334.  
7592633 F.Pio, C.Z.Ni, R.S.Mitchell, J.Knight, S.McKercher, M.Klemsz, A.Lombardo, R.A.Maki, and K.R.Ely (1995).
Co-crystallization of an ETS domain (PU.1) in complex with DNA. Engineering the length of both protein and oligonucleotide.
  J Biol Chem, 270, 24258-24263.  
7744814 J.A.Epstein, P.Lam, L.Jepeal, R.L.Maas, and D.N.Shapiro (1995).
Pax3 inhibits myogenic differentiation of cultured myoblast cells.
  J Biol Chem, 270, 11719-11722.  
  8664547 M.Busslinger, and P.Urbánek (1995).
The role of BSAP (Pax-5) in B-cell development.
  Curr Opin Genet Dev, 5, 595-601.  
  7739566 T.Czerny, and M.Busslinger (1995).
DNA-binding and transactivation properties of Pax-6: three amino acids in the paired domain are responsible for the different sequence recognition of Pax-6 and BSAP (Pax-5).
  Mol Cell Biol, 15, 2858-2871.  
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.