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PDBsum entry 1jgg
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protein dna_rna links
Transcription/DNA PDB id
1jgg

 

 

 

 

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Contents
Protein chains
57 a.a. *
DNA/RNA
Waters ×68
* Residue conservation analysis
PDB id:
1jgg
Name: Transcription/DNA
Title: Even-skipped homeodomain complexed to at-rich DNA
Structure: 5'-d(p Tp Ap Ap Tp Tp Gp Ap Ap Tp T)-3'. Chain: c. Engineered: yes. 5'-d(p Ap Ap Tp Tp Cp Ap Ap Tp Tp A)-3'. Chain: d. Engineered: yes. Segmentation protein even-skipped. Chain: a, b. Fragment: homeodomain.
Source: Synthetic: yes. Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
2.00Å     R-factor:   0.229     R-free:   0.316
Authors: J.A.Hirsch,A.K.Aggarwal
Key ref: J.A.Hirsch and A.K.Aggarwal (1995). Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity. Embo J, 14, 6280-6291. PubMed id: 8557047
Date:
25-Jun-01     Release date:   06-Jul-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P06602  (EVE_DROME) -  Segmentation protein even-skipped from Drosophila melanogaster
Seq:
Struc: 		376 a.a.
57 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  T-A-A-T-T-G-A-A-T-T 10 bases
  A-A-T-T-C-A-A-T-T-A 10 bases

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
Embo J 14:6280-6291 (1995)
PubMed id: 8557047  
 
 
Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity.
J.A.Hirsch, A.K.Aggarwal.
 
  ABSTRACT  
 
even-skipped is a homeobox gene important in controlling segment patterning in the embryonic fruit fly. Its homeobox encodes a DNA binding domain which binds with similar affinities to two DNA consensus sequences, one AT-rich, the other GC-rich. We describe a crystallographic analysis of the Even-skipped homeodomain complexed to an AT-rich oligonucleotide at 2.0 A resolution. The structure reveals a novel arrangement of two homeodomains bound to one 10 bp DNA sequence in a tandem fashion. This arrangement suggests a mechanism for the homeoproteins' regulatory specificity. In addition, the functionally important residue Gln50 is observed in multiple conformations making direct and water-mediated hydrogen bonds with the DNA bases.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21517872 J.C.Harris, M.Hrmova, S.Lopato, and P.Langridge (2011).
Modulation of plant growth by HD-Zip class I and II transcription factors in response to environmental stimuli.
  New Phytol, 190, 823-837.  
  21118975 K.D.Yokoyama, J.L.Thorne, and G.A.Wray (2011).
Coordinated genome-wide modifications within proximal promoter cis-regulatory elements during vertebrate evolution.
  Genome Biol Evol, 3, 66-74.  
20389279 K.Miyazono, Y.Zhi, Y.Takamura, K.Nagata, K.Saigo, T.Kojima, and M.Tanokura (2010).
Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless.
  EMBO J, 29, 1613-1623.
PDB codes: 3a01 3a02 3a03 3lnq
18187506 P.K.Purbey, S.Singh, P.P.Kumar, S.Mehta, K.N.Ganesh, D.Mitra, and S.Galande (2008).
PDZ domain-mediated dimerization and homeodomain-directed specificity are required for high-affinity DNA binding by SATB1.
  Nucleic Acids Res, 36, 2107-2122.  
17981120 R.Joshi, J.M.Passner, R.Rohs, R.Jain, A.Sosinsky, M.A.Crickmore, V.Jacob, A.K.Aggarwal, B.Honig, and R.S.Mann (2007).
Functional specificity of a Hox protein mediated by the recognition of minor groove structure.
  Cell, 131, 530-543.
PDB codes: 2r5y 2r5z
16555308 E.Fodor, and A.Ginsburg (2006).
Specific DNA binding by the homeodomain Nkx2.5(C56S): detection of impaired DNA or unfolded protein by isothermal titration calorimetry.
  Proteins, 64, 13-18.  
15468320 A.Gutmanas, and M.Billeter (2004).
Specific DNA recognition by the Antp homeodomain: MD simulations of specific and nonspecific complexes.
  Proteins, 57, 772-782.  
15226305 B.Pérez-Villamil, M.Mirasierra, and M.Vallejo (2004).
The homeoprotein Alx3 contains discrete functional domains and exhibits cell-specific and selective monomeric binding and transactivation.
  J Biol Chem, 279, 38062-38071.  
12923178 E.J.Stollar, U.Mayor, S.C.Lovell, L.Federici, S.M.Freund, A.R.Fersht, and B.F.Luisi (2003).
Crystal structures of engrailed homeodomain mutants: implications for stability and dynamics.
  J Biol Chem, 278, 43699-43708.
PDB codes: 1p7i 1p7j
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
12548619 W.Flader, B.Wellenzohn, R.H.Winger, A.Hallbrucker, E.Mayer, and K.R.Liedl (2003).
Stepwise induced fit in the pico- to nanosecond time scale governs the complexation of the even-skipped transcriptional repressor homeodomain to DNA.
  Biopolymers, 68, 139-149.  
11847127 T.K.Chiu, C.Sohn, R.E.Dickerson, and R.C.Johnson (2002).
Testing water-mediated DNA recognition by the Hin recombinase.
  EMBO J, 21, 801-814.
PDB codes: 1ijw 1ik2 1ikz 1il7 1ili 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.
  Nucleic Acids Res, 30, 1182-1191.  
11668629 A.V.D'Elia, G.Tell, I.Paron, L.Pellizzari, R.Lonigro, and G.Damante (2001).
Missense mutations of human homeoboxes: A review.
  Hum Mutat, 18, 361-374.  
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
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.  
10075930 A.Carr, and M.D.Biggin (1999).
A comparison of in vivo and in vitro DNA-binding specificities suggests a new model for homeoprotein DNA binding in Drosophila embryos.
  EMBO J, 18, 1598-1608.  
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
  10398683 H.D.Ryoo, and R.S.Mann (1999).
The control of trunk Hox specificity and activity by Extradenticle.
  Genes Dev, 13, 1704-1716.  
10535945 M.Schade, C.J.Turner, R.Kühne, P.Schmieder, K.Lowenhaupt, A.Herbert, A.Rich, and H.Oschkinat (1999).
The solution structure of the Zalpha domain of the human RNA editing enzyme ADAR1 reveals a prepositioned binding surface for Z-DNA.
  Proc Natl Acad Sci U S A, 96, 12465-12470.
PDB code: 1qgp
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.  
10512803 S.Sen, and L.Nilsson (1999).
Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation.
  Biophys J, 77, 1782-1800.  
  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.  
9736453 A.Chariot, S.Senterre-Lesenfants, M.E.Sobel, and V.Castronovo (1998).
Molecular cloning of a mutated HOXB7 cDNA encoding a truncated transactivating homeodomain-containing protein.
  J Cell Biochem, 71, 46-54.  
  9632760 C.Li, and J.L.Manley (1998).
Even-skipped represses transcription by binding TATA binding protein and blocking the TFIID-TATA box interaction.
  Mol Cell Biol, 18, 3771-3781.  
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
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
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.  
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.  
9241421 G.Patikoglou, and S.K.Burley (1997).
Eukaryotic transcription factor-DNA complexes.
  Annu Rev Biophys Biomol Struct, 26, 289-325.  
9032063 J.W.Schwabe (1997).
The role of water in protein-DNA interactions.
  Curr Opin Struct Biol, 7, 126-134.  
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.  
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.  
9368066 P.Arlotta, A.Rustighi, F.Mantovani, G.Manfioletti, V.Giancotti, G.Tell, and G.Damante (1997).
High mobility group I proteins interfere with the homeodomains binding to DNA.
  J Biol Chem, 272, 29904-29910.  
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.  
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.  
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.  
  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.  
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.  
  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.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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