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PDBsum entry 1yuj

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protein dna_rna metals links
DNA binding protein/DNA PDB id
1yuj
Jmol
Contents
Protein chain
54 a.a.
DNA/RNA
Metals
_ZN
PDB id:
1yuj
Name: DNA binding protein/DNA
Title: Solution nmr structure of the gaga factor/DNA complex, 50 structures
Structure: DNA (5'-d( Gp Cp Cp Gp Ap Gp Ap Gp Tp Ap C)-3'). Chain: b. Engineered: yes. DNA (5'-d( Gp Tp Ap Cp Tp Cp Tp Cp Gp Gp C)-3'). Chain: c. Engineered: yes. Gaga-factor. Chain: a. Fragment: DNA binding domain, residues 310 - 372
Source: Synthetic: yes. Drosophila melanogaster. Fruit fly. Organism_taxid: 7227
NMR struc: 50 models
Authors: G.M.Clore,J.G.Omichinski,A.M.Gronenborn
Key ref: J.G.Omichinski et al. (1997). The solution structure of a specific GAGA factor-DNA complex reveals a modular binding mode. Nat Struct Biol, 4, 122-132. PubMed id: 9033593
Date:
31-Dec-96     Release date:   31-Dec-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q08605  (GAGA_DROME) -  Transcription factor GAGA
Seq:
Struc:
 
Seq:
Struc:
581 a.a.
54 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleic acid binding     2 terms  

 

 
Nat Struct Biol 4:122-132 (1997)
PubMed id: 9033593  
 
 
The solution structure of a specific GAGA factor-DNA complex reveals a modular binding mode.
J.G.Omichinski, P.V.Pedone, G.Felsenfeld, A.M.Gronenborn, G.M.Clore.
 
  ABSTRACT  
 
The structure of a complex between the DNA binding domain of the GAGA factor (GAGA-DBD) and an oligonucleotide containing its GAGAG consensus binding site has been determined by nuclear magnetic resonance spectroscopy. The GAGA-DBD comprises a single classical Cys2-His2 zinc finger core, and an N-terminal extension containing two highly basic regions, BR1 and BR2. The zinc finger core binds in the major groove and recognizes the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. Unlike the latter, which require tandem zinc finger repeats with a minimum of two units for high affinity binding, the GAGA-DBD makes use of only a single finger complemented by BR1 and BR2. BR2 forms a helix that interacts in the major groove recognizing the last G of the consensus, while BR1 wraps around the DNA in the minor groove and recognizes the A in the fourth position of the consensus. The implications of the structure of the GAGA-DBD-DNA complex for chromatin remodelling are discussed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20106974 Y.Yang, Q.X.Hua, J.Liu, E.H.Shimizu, M.H.Choquette, R.B.Mackin, and M.A.Weiss (2010).
Solution structure of proinsulin: connecting domain flexibility and prohormone processing.
  J Biol Chem, 285, 7847-7851.
PDB code: 2kqp
19580678 E.Krzywinska, and J.Krzywinski (2009).
Analysis of expression in the Anopheles gambiae developing testes reveals rapidly evolving lineage-specific genes in mosquitoes.
  BMC Genomics, 10, 300.  
19369210 I.Baglivo, L.Russo, S.Esposito, G.Malgieri, M.Renda, A.Salluzzo, B.Di Blasio, C.Isernia, R.Fattorusso, and P.V.Pedone (2009).
The structural role of the zinc ion can be dispensable in prokaryotic zinc-finger domains.
  Proc Natl Acad Sci U S A, 106, 6933-6938.  
17967881 T.R.Menheniott, K.Woodfine, R.Schulz, A.J.Wood, D.Monk, A.S.Giraud, H.S.Baldwin, G.E.Moore, and R.J.Oakey (2008).
Genomic imprinting of Dopa decarboxylase in heart and reciprocal allelic expression with neighboring Grb10.
  Mol Cell Biol, 28, 386-396.  
18184648 Y.Yang, W.Zhang, J.R.Bayrer, and M.A.Weiss (2008).
Doublesex and the regulation of sexual dimorphism in Drosophila melanogaster: structure, function, and mutagenesis of a female-specific domain.
  J Biol Chem, 283, 7280-7292.
PDB codes: 2jz0 2jz1
17956987 G.Malgieri, L.Russo, S.Esposito, I.Baglivo, L.Zaccaro, E.M.Pedone, B.Di Blasio, C.Isernia, P.V.Pedone, and R.Fattorusso (2007).
The prokaryotic Cys2His2 zinc-finger adopts a novel fold as revealed by the NMR structure of Agrobacterium tumefaciens Ros DNA-binding domain.
  Proc Natl Acad Sci U S A, 104, 17341-17346.
PDB code: 2jsp
17947335 J.Bernués, D.Piñeyro, and A.Kosoy (2007).
General, negative feedback mechanism for regulation of Trithorax-like gene expression in vivo: new roles for GAGA factor in flies.
  Nucleic Acids Res, 35, 7150-7159.  
16936828 N.L.Adkins, T.A.Hagerman, and P.Georgel (2006).
GAGA protein: a multi-faceted transcription factor.
  Biochem Cell Biol, 84, 559-567.  
16962967 P.Prabakaran, J.G.Siebers, S.Ahmad, M.M.Gromiha, M.G.Singarayan, and A.Sarai (2006).
Classification of protein-DNA complexes based on structural descriptors.
  Structure, 14, 1355-1367.  
16521086 S.Negi, M.Dhanasekaran, T.Hirata, H.Urata, and Y.Sugiura (2006).
Biomolecular mirror-image recognition: reciprocal chiral-specific DNA binding of synthetic enantiomers of zinc finger domain from GAGA factor.
  Chirality, 18, 254-258.  
16084393 I.Friedberg, and A.Godzik (2005).
Connecting the protein structure universe by using sparse recurring fragments.
  Structure, 13, 1213-1224.  
15608118 S.Hanaoka, A.Nagadoi, and Y.Nishimura (2005).
Comparison between TRF2 and TRF1 of their telomeric DNA-bound structures and DNA-binding activities.
  Protein Sci, 14, 119-130.
PDB codes: 1vf9 1vfc
14709556 A.P.Runko, and C.G.Sagerström (2004).
Isolation of nlz2 and characterization of essential domains in Nlz family proteins.
  J Biol Chem, 279, 11917-11925.  
15492775 J.Gaudet, S.Muttumu, M.Horner, and S.E.Mango (2004).
Whole-genome analysis of temporal gene expression during foregut development.
  PLoS Biol, 2, e352.  
15247335 J.W.Pham, I.Radhakrishnan, and E.J.Sontheimer (2004).
Thermodynamic and structural characterization of 2'-nitrogen-modified RNA duplexes.
  Nucleic Acids Res, 32, 3446-3455.  
15326190 M.J.Morgan, J.M.Woltering, P.M.In der Rieden, A.J.Durston, and J.P.Thiery (2004).
YY1 regulates the neural crest-associated slug gene in Xenopus laevis.
  J Biol Chem, 279, 46826-46834.  
15449319 M.Nakamura, A.P.Runko, and C.G.Sagerström (2004).
A novel subfamily of zinc finger genes involved in embryonic development.
  J Cell Biochem, 93, 887-895.  
15579691 S.Schweinsberg, K.Hagstrom, D.Gohl, P.Schedl, R.P.Kumar, R.Mishra, and F.Karch (2004).
The enhancer-blocking activity of the Fab-7 boundary from the Drosophila bithorax complex requires GAGA-factor-binding sites.
  Genetics, 168, 1371-1384.  
12601174 B.van Steensel, J.Delrow, and H.J.Bussemaker (2003).
Genomewide analysis of Drosophila GAGA factor target genes reveals context-dependent DNA binding.
  Proc Natl Acad Sci U S A, 100, 2580-2585.  
12616630 C.Isernia, E.Bucci, M.Leone, L.Zaccaro, P.Di Lello, G.Digilio, S.Esposito, M.Saviano, B.Di Blasio, C.Pedone, P.V.Pedone, and R.Fattorusso (2003).
NMR structure of the single QALGGH zinc finger domain from the Arabidopsis thaliana SUPERMAN protein.
  Chembiochem, 4, 171-180.
PDB code: 1njq
12876199 L.V.Sun, L.Chen, F.Greil, N.Negre, T.R.Li, G.Cavalli, H.Zhao, B.Van Steensel, and K.P.White (2003).
Protein-DNA interaction mapping using genomic tiling path microarrays in Drosophila.
  Proc Natl Acad Sci U S A, 100, 9428-9433.  
12200449 A.Kosoy, S.Pagans, M.L.Espinas, F.Azorin, and J.Bernues (2002).
GAGA factor down-regulates its own promoter.
  J Biol Chem, 277, 42280-42288.  
12119013 C.Brenner (2002).
Hint, Fhit, and GalT: function, structure, evolution, and mechanism of three branches of the histidine triad superfamily of nucleotide hydrolases and transferases.
  Biochemistry, 41, 9003-9014.  
11867548 J.Iwahara, M.Iwahara, G.W.Daughdrill, J.Ford, and R.T.Clubb (2002).
The structure of the Dead ringer-DNA complex reveals how AT-rich interaction domains (ARIDs) recognize DNA.
  EMBO J, 21, 1197-1209.
PDB code: 1kqq
12433998 N.Dathan, L.Zaccaro, S.Esposito, C.Isernia, J.G.Omichinski, A.Riccio, C.Pedone, B.Di Blasio, R.Fattorusso, and P.V.Pedone (2002).
The Arabidopsis SUPERMAN protein is able to specifically bind DNA through its single Cys2-His2 zinc finger motif.
  Nucleic Acids Res, 30, 4945-4951.  
11713290 A.J.Greenberg, and P.Schedl (2001).
GAGA factor isoforms have distinct but overlapping functions in vivo.
  Mol Cell Biol, 21, 8565-8574.  
11395410 C.O.Pabo, E.Peisach, and R.A.Grant (2001).
Design and selection of novel Cys2His2 zinc finger proteins.
  Annu Rev Biochem, 70, 313-340.  
11371345 I.Ohki, N.Shimotake, N.Fujita, J.Jee, T.Ikegami, M.Nakao, and M.Shirakawa (2001).
Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA.
  Cell, 105, 487-497.
PDB code: 1ig4
11742991 L.J.Lambert, V.Schirf, B.Demeler, M.Cadene, and M.H.Werner (2001).
Flipping a genetic switch by subunit exchange.
  EMBO J, 20, 7149-7159.
PDB codes: 1ka3 1tkv
11500367 M.Cai, Y.Huang, R.Ghirlando, K.L.Wilson, R.Craigie, and G.M.Clore (2001).
Solution structure of the constant region of nuclear envelope protein LAP2 reveals two LEM-domain structures: one binds BAF and the other binds DNA.
  EMBO J, 20, 4399-4407.
PDB code: 1gjj
10716920 G.Barbato, D.O.Cicero, F.Cordier, F.Narjes, B.Gerlach, S.Sambucini, S.Grzesiek, V.G.Matassa, R.De Francesco, and R.Bazzo (2000).
Inhibitor binding induces active site stabilization of the HCV NS3 protein serine protease domain.
  EMBO J, 19, 1195-1206.
PDB code: 1dxw
11060015 G.Wang, J.M.Louis, M.Sondej, Y.J.Seok, A.Peterkofsky, and G.M.Clore (2000).
Solution structure of the phosphoryl transfer complex between the signal transducing proteins HPr and IIA(glucose) of the Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system.
  EMBO J, 19, 5635-5649.
PDB code: 1ggr
10835359 K.Huang, J.M.Louis, L.Donaldson, F.L.Lim, A.D.Sharrocks, and G.M.Clore (2000).
Solution structure of the MEF2A-DNA complex: structural basis for the modulation of DNA bending and specificity by MADS-box transcription factors.
  EMBO J, 19, 2615-2628.
PDB code: 1c7u
10773080 M.Schaub, A.Krol, and P.Carbon (2000).
Structural organization of Staf-DNA complexes.
  Nucleic Acids Res, 28, 2114-2121.  
10940247 S.A.Wolfe, L.Nekludova, and C.O.Pabo (2000).
DNA recognition by Cys2His2 zinc finger proteins.
  Annu Rev Biophys Biomol Struct, 29, 183-212.  
11106741 S.Janssen, O.Cuvier, M.Müller, and U.K.Laemmli (2000).
Specific gain- and loss-of-function phenotypes induced by satellite-specific DNA-binding drugs fed to Drosophila melanogaster.
  Mol Cell, 6, 1013-1024.  
9927429 K.R.Katsani, M.A.Hajibagheri, and C.P.Verrijzer (1999).
Co-operative DNA binding by GAGA transcription factor requires the conserved BTB/POZ domain and reorganizes promoter topology.
  EMBO J, 18, 698-708.  
10446199 M.Schaub, A.Krol, and P.Carbon (1999).
Flexible zinc finger requirement for binding of the transcriptional activator staf to U6 small nuclear RNA and tRNA(Sec) promoters.
  J Biol Chem, 274, 24241-24249.  
9733760 E.Jiménez-García, A.Vaquero, M.L.Espinás, R.Soliva, M.Orozco, J.Bernués, and F.Azorín (1998).
The GAGA factor of Drosophila binds triple-stranded DNA.
  J Biol Chem, 273, 24640-24648.  
9705341 E.Myslinski, A.Krol, and P.Carbon (1998).
ZNF76 and ZNF143 are two human homologs of the transcriptional activator Staf.
  J Biol Chem, 273, 21998-22006.  
9600889 G.M.Clore, and A.M.Gronenborn (1998).
New methods of structure refinement for macromolecular structure determination by NMR.
  Proc Natl Acad Sci U S A, 95, 5891-5898.  
9478126 J.P.Mackay, and M.Crossley (1998).
Zinc fingers are sticking together.
  Trends Biochem Sci, 23, 1-4.  
9508764 J.S.Platero, A.K.Csink, A.Quintanilla, and S.Henikoff (1998).
Changes in chromosomal localization of heterochromatin-binding proteins during the cell cycle in Drosophila.
  J Cell Biol, 140, 1297-1306.  
9646872 K.H.Gardner, and L.E.Kay (1998).
The use of 2H, 13C, 15N multidimensional NMR to study the structure and dynamics of proteins.
  Annu Rev Biophys Biomol Struct, 27, 357-406.  
9736626 M.D.Allen, K.Yamasaki, M.Ohme-Takagi, M.Tateno, and M.Suzuki (1998).
A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA.
  EMBO J, 17, 5484-5496.
PDB codes: 1gcc 2gcc 3gcc
9665172 P.Agback, H.Baumann, S.Knapp, R.Ladenstein, and T.Härd (1998).
Architecture of nonspecific protein-DNA interactions in the Sso7d-DNA complex.
  Nat Struct Biol, 5, 579-584.
PDB code: 1bbx
9592153 R.C.Wilkins, and J.T.Lis (1998).
GAGA factor binding to DNA via a single trinucleotide sequence element.
  Nucleic Acids Res, 26, 2672-2678.  
9539107 R.Gherzi, A.Leprini, A.Siri, and L.Zardi (1998).
Structure of 5' region of human tenascin-R gene and characterization of its promoter.
  DNA Cell Biol, 17, 275-282.  
  9808619 S.Ohtsuki, and M.Levine (1998).
GAGA mediates the enhancer blocking activity of the eve promoter in the Drosophila embryo.
  Genes Dev, 12, 3325-3330.  
9519295 S.Tan, and T.J.Richmond (1998).
Eukaryotic transcription factors.
  Curr Opin Struct Biol, 8, 41-48.  
9224603 A.L.Vuidepot, F.Bontems, M.Gervais, B.Guiard, E.Shechter, and J.Y.Lallemand (1997).
NMR analysis of CYP1(HAP1) DNA binding domain-CYC1 upstream activation sequence interactions: recognition of a CGG trinucleotide and of an additional thymine 5 bp downstream by the zinc cluster and the N-terminal extremity of the protein.
  Nucleic Acids Res, 25, 3042-3050.  
9659911 G.Mizuguchi, T.Tsukiyama, J.Wisniewski, and C.Wu (1997).
Role of nucleosome remodeling factor NURF in transcriptional activation of chromatin.
  Mol Cell, 1, 141-150.  
  9385638 J.R.Huth, C.A.Bewley, B.M.Jackson, A.G.Hinnebusch, G.M.Clore, and A.M.Gronenborn (1997).
Design of an expression system for detecting folded protein domains and mapping macromolecular interactions by NMR.
  Protein Sci, 6, 2359-2364.  
9253416 J.R.Huth, C.A.Bewley, M.S.Nissen, J.N.Evans, R.Reeves, A.M.Gronenborn, and G.M.Clore (1997).
The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif.
  Nat Struct Biol, 4, 657-665.
PDB codes: 2ezd 2eze 2ezf 2ezg
  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.  
9184231 P.V.Pedone, J.G.Omichinski, P.Nony, C.Trainor, A.M.Gronenborn, G.M.Clore, and G.Felsenfeld (1997).
The N-terminal fingers of chicken GATA-2 and GATA-3 are independent sequence-specific DNA binding domains.
  EMBO J, 16, 2874-2882.  
9321643 R.C.Wilkins, and J.T.Lis (1997).
Dynamics of potentiation and activation: GAGA factor and its role in heat shock gene regulation.
  Nucleic Acids Res, 25, 3963-3968.  
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.