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PDBsum entry 2drp
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protein dna_rna metals Protein-protein interface(s) links
Transcription/DNA PDB id
2drp

 

 

 

 

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Contents
Protein chains
63 a.a. *
DNA/RNA
Metals
_ZN ×4
Waters ×57
* Residue conservation analysis
PDB id:
2drp
Name: Transcription/DNA
Title: The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition
Structure: DNA (5'- d( Cp Tp Ap Ap Tp Ap Ap Gp Gp Ap Tp Ap Ap Cp Gp Tp C p Cp G)-3'). Chain: b, e. Engineered: yes. DNA (5'- d( Tp Cp Gp Gp Ap Cp Gp Tp Tp Ap Tp Cp Cp Tp Tp Ap T p Tp A)-3'). Chain: c, f. Engineered: yes. Protein (tramtrack DNA-binding domain).
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:   0.193    
Authors: L.Fairall,J.W.R.Schwabe,L.Chapman,J.T.Finch,D.Rhodes
Key ref: L.Fairall et al. (1993). The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition. Nature, 366, 483-487. PubMed id: 8247159
Date:
06-Jun-94     Release date:   31-Aug-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P17789  (TTKB_DROME) -  Protein tramtrack, beta isoform from Drosophila melanogaster
Seq:
Struc: 		 
Seq:
Struc: 		643 a.a.
63 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains
  C-T-A-A-T-A-A-G-G-A-T-A-A-C-G-T-C-C-G 19 bases
  T-C-G-G-A-C-G-T-T-A-T-C-C-T-T-A-T-T-A 19 bases
  C-T-A-A-T-A-A-G-G-A-T-A-A-C-G-T-C-C-G 19 bases
  T-C-G-G-A-C-G-T-T-A-T-C-C-T-T-A-T-T-A 19 bases

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

 

 
Nature 366:483-487 (1993)
PubMed id: 8247159  
 
 
The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition.
L.Fairall, J.W.Schwabe, L.Chapman, J.T.Finch, D.Rhodes.
 
  ABSTRACT  
 
The Cys2-His2 zinc-finger is the most widely occurring DNA-binding motif. The first structure of a zinc-finger/DNA complex revealed a fairly simple mechanism for DNA recognition suggesting that the zinc-finger might represent a candidate template for designing proteins to recognize DNA. Residues at three key positions in an alpha-helical 'reading head' play a dominant role in base-recognition and have been targets for mutagenesis experiments aimed at deriving a recognition code. Here we report the structure of a two zinc-finger DNA-binding domain from the protein Tramtrack complexed with DNA. The amino-terminal zinc-finger and its interaction with DNA illustrate several novel features. These include the use of a serine residue, which is semi-conserved and located outside the three key positions, to make a base contact. Its role in base-recognition correlates with a large, local, protein-induced deformation of the DNA helix at a flexible A-T-A sequence and may give insight into previous mutagenesis experiments. It is apparent from this structure that zinc-finger/DNA recognition is more complex than was originally perceived.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20658568 B.Yang, Y.Zhu, Y.Wang, and G.Chen (2011).
Interaction identification of Zif268 and TATA(ZF) proteins with GC-/AT-rich DNA sequence: A theoretical study.
  J Comput Chem, 32, 416-428.  
20478078 A.Klug (2010).
The discovery of zinc fingers and their development for practical applications in gene regulation and genome manipulation.
  Q Rev Biophys, 43, 1.  
20192761 A.Klug (2010).
The discovery of zinc fingers and their applications in gene regulation and genome manipulation.
  Annu Rev Biochem, 79, 213-231.  
20047959 A.N.Temiz, P.V.Benos, and C.J.Camacho (2010).
Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains.
  Nucleic Acids Res, 38, 2134-2144.  
20544958 C.C.Chou, Y.C.Lou, T.K.Tang, and C.Chen (2010).
Structure and DNA binding characteristics of the three-Cys(2)His(2) domain of mouse testis zinc finger protein.
  Proteins, 78, 2202-2212.  
20717154 F.D.Urnov, E.J.Rebar, M.C.Holmes, H.S.Zhang, and P.D.Gregory (2010).
Genome editing with engineered zinc finger nucleases.
  Nat Rev Genet, 11, 636-646.  
20231359 R.Iida, M.Ueki, and T.Yasuda (2010).
A novel transcriptional repressor, Rhit, is involved in heat-inducible and age-dependent expression of Mpv17-like protein, a participant in reactive oxygen species metabolism.
  Mol Cell Biol, 30, 2306-2315.  
20334529 R.Rohs, X.Jin, S.M.West, R.Joshi, B.Honig, and R.S.Mann (2010).
Origins of specificity in protein-DNA recognition.
  Annu Rev Biochem, 79, 233-269.  
19429892 N.A.Temiz, and C.J.Camacho (2009).
Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface.
  Nucleic Acids Res, 37, 4076-4088.  
18586699 J.Liu, and G.D.Stormo (2008).
Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors.
  Bioinformatics, 24, 1850-1857.  
18673565 T.Brody, W.Rasband, K.Baler, A.Kuzin, M.Kundu, and W.F.Odenwald (2008).
Sequence conservation and combinatorial complexity of Drosophila neural precursor cell enhancers.
  BMC Genomics, 9, 371.  
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
17626045 K.Rothfels, O.Rowland, and J.Segall (2007).
Zinc fingers 1 and 7 of yeast TFIIIA are essential for assembly of a functional transcription complex on the 5 S RNA gene.
  Nucleic Acids Res, 35, 4869-4881.  
17490485 T.Brody, W.Rasband, K.Baler, A.Kuzin, M.Kundu, and W.F.Odenwald (2007).
cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers.
  Genome Biol, 8, R75.  
17088325 B.W.Berger, C.M.Gendron, A.M.Lenhoff, and E.W.Kaler (2006).
Effects of additives on surfactant phase behavior relevant to bacteriorhodopsin crystallization.
  Protein Sci, 15, 2682-2696.  
16107335 B.Dreier, R.P.Fuller, D.J.Segal, C.V.Lund, P.Blancafort, A.Huber, B.Koksch, and C.F.Barbas (2005).
Development of zinc finger domains for recognition of the 5'-CNN-3' family DNA sequences and their use in the construction of artificial transcription factors.
  J Biol Chem, 280, 35588-35597.  
15713659 K.L.Brady, and D.R.Setzer (2005).
Is there a dynamic DNA-protein interface in the transcription factor IIIA-5 S rRNA gene complex?
  J Biol Chem, 280, 16115-16124.  
15557258 M.J.Lachenmann, J.E.Ladbury, X.Qian, K.Huang, R.Singh, and M.A.Weiss (2004).
Solvation and the hidden thermodynamics of a zinc finger probed by nonstandard repair of a protein crevice.
  Protein Sci, 13, 3115-3126.
PDB code: 1xrz
14978306 P.Gutiérrez, M.J.Osborne, N.Siddiqui, J.F.Trempe, C.Arrowsmith, and K.Gehring (2004).
Structure of the archaeal translation initiation factor aIF2 beta from Methanobacterium thermoautotrophicum: implications for translation initiation.
  Protein Sci, 13, 659-667.
PDB code: 1nee
12750739 A.C.Jamieson, J.C.Miller, and C.O.Pabo (2003).
Drug discovery with engineered zinc-finger proteins.
  Nat Rev Drug Discov, 2, 361-368.  
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
12804117 H.R.Chrisman, and D.J.Tindall (2003).
Identification and characterization of a consensus DNA binding element for the zinc finger transcription factor TIEG/EGRalpha.
  DNA Cell Biol, 22, 187-199.  
12574501 M.Papworth, M.Moore, M.Isalan, M.Minczuk, Y.Choo, and A.Klug (2003).
Inhibition of herpes simplex virus 1 gene expression by designer zinc-finger transcription factors.
  Proc Natl Acad Sci U S A, 100, 1621-1626.  
12897852 Z.Yang, and J.J.Hayes (2003).
Xenopus transcription factor IIIA and the 5S nucleosome: development of a useful in vitro system.
  Biochem Cell Biol, 81, 177-184.  
12193271 C.E.Allen, C.H.Mak, and L.C.Wu (2002).
The kappa B transcriptional enhancer motif and signal sequences of V(D)J recombination are targets for the zinc finger protein HIVEP3/KRC: a site selection amplification binding study.
  BMC Immunol, 3, 10.  
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.  
11726671 Q.Liu, Z.Xia, X.Zhong, and C.C.Case (2002).
Validated zinc finger protein designs for all 16 GNN DNA triplet targets.
  J Biol Chem, 277, 3850-3856.  
11154279 B.Gebelein, and R.Urrutia (2001).
Sequence-specific transcriptional repression by KS1, a multiple-zinc-finger-Krüppel-associated box protein.
  Mol Cell Biol, 21, 928-939.  
11390978 C.K.Hwang, U.M.D'Souza, A.J.Eisch, S.Yajima, C.H.Lammers, Y.Yang, S.H.Lee, Y.M.Kim, E.J.Nestler, and M.M.Mouradian (2001).
Dopamine receptor regulating factor, DRRF: a zinc finger transcription factor.
  Proc Natl Acad Sci U S A, 98, 7558-7563.  
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.  
11554446 D.P.Giedroc, X.Chen, and J.L.Apuy (2001).
Metal response element (MRE)-binding transcription factor-1 (MTF-1): structure, function, and regulation.
  Antioxid Redox Signal, 3, 577-596.  
11456999 J.W.Chin, and A.Schepartz (2001).
Concerted evolution of structure and function in a miniature protein.
  J Am Chem Soc, 123, 2929-2930.  
11258905 M.Nagaoka, T.Kaji, M.Imanishi, Y.Hori, W.Nomura, and Y.Sugiura (2001).
Multiconnection of identical zinc finger: implication for DNA binding affinity and unit modulation of the three zinc finger domain.
  Biochemistry, 40, 2932-2941.  
11583159 W.Schüler, K.Kloiber, T.Matt, K.Bister, and R.Konrat (2001).
Application of cross-correlated NMR spin relaxation to the zinc-finger protein CRP2(LIM2): evidence for collective motions in LIM domains.
  Biochemistry, 40, 9596-9604.
PDB code: 1ibi
11327841 Y.Uno, K.Matsushita, M.Nagaoka, and Y.Sugiura (2001).
Finger-positional change in three zinc finger protein Sp1: influence of terminal finger in DNA recognition.
  Biochemistry, 40, 1787-1795.  
10642181 E.T.Young, N.Kacherovsky, and C.Cheng (2000).
An accessory DNA binding motif in the zinc finger protein Adr1 assists stable binding to DNA and can be replaced by a third finger.
  Biochemistry, 39, 567-574.  
11018257 I.W.Manfield, L.A.Reynolds, J.Gittins, and G.G.Kneale (2000).
The DNA-binding domain of the gene regulatory protein AreA extends beyond the minimal zinc-finger region conserved between GATA proteins.
  Biochim Biophys Acta, 1493, 325-332.  
10773080 M.Schaub, A.Krol, and P.Carbon (2000).
Structural organization of Staf-DNA complexes.
  Nucleic Acids Res, 28, 2114-2121.  
  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.  
10675317 P.Nissen, M.Kjeldgaard, and J.Nyborg (2000).
Macromolecular mimicry.
  EMBO J, 19, 489-495.  
10903945 S.A.Wolfe, E.I.Ramm, and C.O.Pabo (2000).
Combining structure-based design with phage display to create new Cys(2)His(2) zinc finger dimers.
  Structure, 8, 739-750.  
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.  
10449725 D.J.McColl, C.D.Honchell, and A.D.Frankel (1999).
Structure-based design of an RNA-binding zinc finger.
  Proc Natl Acad Sci U S A, 96, 9521-9526.  
10077584 D.J.Segal, B.Dreier, R.R.Beerli, and C.F.Barbas (1999).
Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences.
  Proc Natl Acad Sci U S A, 96, 2758-2763.  
10026283 K.Nadassy, S.J.Wodak, and J.Janin (1999).
Structural features of protein-nucleic acid recognition sites.
  Biochemistry, 38, 1999-2017.  
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.  
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.  
9651329 G.Roesijadi, R.Bogumil, M.Vasák, and J.H.Kägi (1998).
Modulation of DNA binding of a tramtrack zinc finger peptide by the metallothionein-thionein conjugate pair.
  J Biol Chem, 273, 17425-17432.  
9786867 H.Zhao, E.Butler, J.Rodgers, T.Spizzo, S.Duesterhoeft, and D.Eide (1998).
Regulation of zinc homeostasis in yeast by binding of the ZAP1 transcriptional activator to zinc-responsive promoter elements.
  J Biol Chem, 273, 28713-28720.  
9665182 J.H.Prestegard (1998).
New techniques in structural NMR--anisotropic interactions.
  Nat Struct Biol, 5, 517-522.  
9467467 J.L.Pomerantz, S.A.Wolfe, and C.O.Pabo (1998).
Structure-based design of a dimeric zinc finger protein.
  Biochemistry, 37, 965-970.  
  9528759 J.M.Madison, A.M.Dudley, and F.Winston (1998).
Identification and analysis of Mot3, a zinc finger protein that binds to the retrotransposon Ty long terminal repeat (delta) in Saccharomyces cerevisiae.
  Mol Cell Biol, 18, 1879-1890.  
9421523 K.Kubo, A.Sakamoto, A.Kobayashi, Z.Rybka, Y.Kanno, H.Nakagawa, and H.Takatsuji (1998).
Cys2/His2 zinc-finger protein family of petunia: evolution and general mechanism of target-sequence recognition.
  Nucleic Acids Res, 26, 608-615.  
9562555 M.Elrod-Erickson, T.E.Benson, and C.O.Pabo (1998).
High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition.
  Structure, 6, 451-464.
PDB codes: 1a1f 1a1g 1a1h 1a1i 1a1j 1a1k 1a1l
9724513 M.Isalan, A.Klug, and Y.Choo (1998).
Comprehensive DNA recognition through concerted interactions from adjacent zinc fingers.
  Biochemistry, 37, 12026-12033.  
9580682 M.Shimizu, W.Li, P.A.Covitz, M.Hara, H.Shindo, and A.P.Mitchell (1998).
Genomic footprinting of the yeast zinc finger protein Rme1p and its roles in repression of the meiotic activator IME1.
  Nucleic Acids Res, 26, 2329-2336.  
9578568 M.Yokono, N.Saegusa, K.Matsushita, and Y.Sugiura (1998).
Unique DNA binding mode of the N-terminal zinc finger of transcription factor Sp1.
  Biochemistry, 37, 6824-6832.  
9443960 R.F.Ryan, and M.K.Darby (1998).
The role of zinc finger linkers in p43 and TFIIIA binding to 5S rRNA and DNA.
  Nucleic Acids Res, 26, 703-709.  
  9436984 R.Kambadur, K.Koizumi, C.Stivers, J.Nagle, S.J.Poole, and W.F.Odenwald (1998).
Regulation of POU genes by castor and hunchback establishes layered compartments in the Drosophila CNS.
  Genes Dev, 12, 246-260.  
9501194 R.T.Nolte, R.M.Conlin, S.C.Harrison, and R.S.Brown (1998).
Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex.
  Proc Natl Acad Sci U S A, 95, 2938-2943.
PDB code: 1tf6
9485332 T.B.Hamilton, F.Borel, and P.J.Romaniuk (1998).
Comparison of the DNA binding characteristics of the related zinc finger proteins WT1 and EGR1.
  Biochemistry, 37, 2051-2058.  
9698361 X.Chen, A.Agarwal, and D.P.Giedroc (1998).
Structural and functional heterogeneity among the zinc fingers of human MRE-binding transcription factor-1.
  Biochemistry, 37, 11152-11161.  
9546210 Y.Choo, and J.W.Schwabe (1998).
All wrapped up.
  Nat Struct Biol, 5, 253-255.  
9421515 Y.Choo (1998).
End effects in DNA recognition by zinc finger arrays.
  Nucleic Acids Res, 26, 554-557.  
9033581 C.M.Read, and P.C.Driscoll (1997).
GAGA over the nucleosome.
  Nat Struct Biol, 4, 87-89.  
9242690 D.G.Kehres, G.S.Subramanyan, V.S.Hung, G.W.Rogers, and D.R.Setzer (1997).
Energetically unfavorable interactions among the zinc fingers of transcription factor IIIA when bound to the 5 S rRNA gene.
  J Biol Chem, 272, 20152-20161.  
  9154812 F.Payre, P.Buono, N.Vanzo, and A.Vincent (1997).
Two types of zinc fingers are required for dimerization of the serendipity delta transcriptional activator.
  Mol Cell Biol, 17, 3137-3145.  
9241421 G.Patikoglou, and S.K.Burley (1997).
Eukaryotic transcription factor-DNA complexes.
  Annu Rev Biophys Biomol Struct, 26, 289-325.  
9005850 H.A.Greisman, and C.O.Pabo (1997).
A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites.
  Science, 275, 657-661.  
9033593 J.G.Omichinski, P.V.Pedone, G.Felsenfeld, A.M.Gronenborn, and G.M.Clore (1997).
The solution structure of a specific GAGA factor-DNA complex reveals a modular binding mode.
  Nat Struct Biol, 4, 122-132.
PDB codes: 1yui 1yuj
9032063 J.W.Schwabe (1997).
The role of water in protein-DNA interactions.
  Curr Opin Struct Biol, 7, 126-134.  
9278395 J.Y.Li, M.A.English, H.J.Ball, P.L.Yeyati, S.Waxman, and J.D.Licht (1997).
Sequence-specific DNA binding and transcriptional regulation by the promyelocytic leukemia zinc finger protein.
  J Biol Chem, 272, 22447-22455.  
9159121 M.Isalan, Y.Choo, and A.Klug (1997).
Synergy between adjacent zinc fingers in sequence-specific DNA recognition.
  Proc Natl Acad Sci U S A, 94, 5617-5621.  
9253405 M.P.Foster, D.S.Wuttke, I.Radhakrishnan, D.A.Case, J.M.Gottesfeld, and P.E.Wright (1997).
Domain packing and dynamics in the DNA complex of the N-terminal zinc fingers of TFIIIA.
  Nat Struct Biol, 4, 605-608.
PDB code: 1tf3
  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.  
9159105 Q.Liu, D.J.Segal, J.B.Ghiara, and C.F.Barbas (1997).
Design of polydactyl zinc-finger proteins for unique addressing within complex genomes.
  Proc Natl Acad Sci U S A, 94, 5525-5530.  
9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
  Biopolymers, 44, 361-403.  
  9121460 V.Arranz, F.Harper, Y.Florentin, E.Puvion, M.Kress, and M.Ernoult-Lange (1997).
Human and mouse MOK2 proteins are associated with nuclear ribonucleoprotein components and bind specifically to RNA and DNA through their zinc finger domains.
  Mol Cell Biol, 17, 2116-2126.  
9053397 W.D.Kohn, C.T.Mant, and R.S.Hodges (1997).
Alpha-helical protein assembly motifs.
  J Biol Chem, 272, 2583-2586.  
9110988 W.J.Friesen, and M.K.Darby (1997).
Phage display of RNA binding zinc fingers from transcription factor IIIA.
  J Biol Chem, 272, 10994-10997.  
9032060 Y.Choo, and A.Klug (1997).
Physical basis of a protein-DNA recognition code.
  Curr Opin Struct Biol, 7, 117-125.  
8918802 A.B.Hegvold, and O.S.Gabrielsen (1996).
The importance of the linker connecting the repeats of the c-Myb oncoprotein may be due to a positioning function.
  Nucleic Acids Res, 24, 3990-3995.  
8917505 A.C.Jamieson, H.Wang, and S.H.Kim (1996).
A zinc finger directory for high-affinity DNA recognition.
  Proc Natl Acad Sci U S A, 93, 12834-12839.  
8901872 C.A.Kim, and J.M.Berg (1996).
A 2.2 A resolution crystal structure of a designed zinc finger protein bound to DNA.
  Nat Struct Biol, 3, 940-945.
PDB code: 1mey
8942976 H.B.Houbaviy, A.Usheva, T.Shenk, and S.K.Burley (1996).
Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator.
  Proc Natl Acad Sci U S A, 93, 13577-13582.
PDB code: 1ubd
8700901 J.A.Gogos, J.Jin, H.Wan, M.Kokkinidis, and F.C.Kafatos (1996).
Recognition of diverse sequences by class I zinc fingers: asymmetries and indirect effects on specificity in the interaction between CF2II and A+T-rich elements.
  Proc Natl Acad Sci U S A, 93, 2159-2164.  
8939742 M.Elrod-Erickson, M.A.Rould, L.Nekludova, and C.O.Pabo (1996).
Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions.
  Structure, 4, 1171-1180.
PDB code: 1aay
8657576 M.L'Haridon, P.Paul, J.G.Xerri, H.Dastot, C.Dolliger, M.Schmid, N.de Angelis, L.Grollet, F.Sigaux, L.Degos, and C.Gazin (1996).
Transcriptional regulation of the MHC class I HLA-A11 promoter by the zinc finger protein ZFX.
  Nucleic Acids Res, 24, 1928-1935.  
8679640 M.Nagaoka, and Y.Sugiura (1996).
Distinct phosphate backbone contacts revealed by some mutant peptides of zinc finger protein Spl: effect of protein-induced bending on DNA recognition.
  Biochemistry, 35, 8761-8768.  
8662611 O.Rowland, and J.Segall (1996).
Interaction of wild-type and truncated forms of transcription factor IIIA from Saccharomyces cerevisiae with the 5 S RNA gene.
  J Biol Chem, 271, 12103-12110.  
9077440 P.Badenhorst, S.Harrison, and A.Travers (1996).
End of the line? Tramtrack and cell fate determination in Drosophila.
  Genes Cells, 1, 707-716.  
8610125 P.V.Pedone, R.Ghirlando, G.M.Clore, A.M.Gronenborn, G.Felsenfeld, and J.G.Omichinski (1996).
The single Cys2-His2 zinc finger domain of the GAGA protein flanked by basic residues is sufficient for high-affinity specific DNA binding.
  Proc Natl Acad Sci U S A, 93, 2822-2826.  
8736557 R.N.Dutnall, D.Neuhaus, and D.Rhodes (1996).
The solution structure of the first zinc finger domain of SWI5: a novel structural extension to a common fold.
  Structure, 4, 599-611.
PDB code: 1ncs
8692697 S.J.McBryant, B.Gedulin, K.R.Clemens, P.E.Wright, and J.M.Gottesfeld (1996).
Assessment of major and minor groove DNA interactions by the zinc fingers of Xenopus transcription factor IIIA.
  Nucleic Acids Res, 24, 2567-2574.  
8577732 Y.G.Kim, J.Cha, and S.Chandrasegaran (1996).
Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain.
  Proc Natl Acad Sci U S A, 93, 1156-1160.  
8563758 Y.Kuroiwa, T.Kaneko-Ishino, F.Kagitani, T.Kohda, L.L.Li, M.Tada, R.Suzuki, M.Yokoyama, T.Shiroishi, S.Wakana, S.C.Barton, F.Ishino, and M.A.Surani (1996).
Peg3 imprinted gene on proximal chromosome 7 encodes for a zinc finger protein.
  Nat Genet, 12, 186-190.  
8620008 Y.Shi, and J.M.Berg (1996).
DNA unwinding induced by zinc finger protein binding.
  Biochemistry, 35, 3845-3848.  
  7891721 A.H.Swirnoff, and J.Milbrandt (1995).
DNA-binding specificity of NGFI-A and related zinc finger transcription factors.
  Mol Cell Biol, 15, 2275-2287.  
  8575189 A.M.Gronenborn, and G.M.Clore (1995).
Structures of protein complexes by multidimensional heteronuclear magnetic resonance spectroscopy.
  Crit Rev Biochem Mol Biol, 30, 351-385.  
7831288 H.Wu, W.P.Yang, and C.F.Barbas (1995).
Building zinc fingers by selection: toward a therapeutic application.
  Proc Natl Acad Sci U S A, 92, 344-348.  
8562282 J.Brandão-Neto, G.Madureira, B.B.Mendonça, W.Bloise, and A.V.Castro (1995).
Endocrine interaction between zinc and prolactin. An interpretative review.
  Biol Trace Elem Res, 49, 139-149.  
  7882981 J.Tilburn, S.Sarkar, D.A.Widdick, E.A.Espeso, M.Orejas, J.Mungroo, M.A.Peñalva, and H.N.Arst (1995).
The Aspergillus PacC zinc finger transcription factor mediates regulation of both acid- and alkaline-expressed genes by ambient pH.
  EMBO J, 14, 779-790.  
7735836 J.W.Schwabe, L.Chapman, and D.Rhodes (1995).
The oestrogen receptor recognizes an imperfectly palindromic response element through an alternative side-chain conformation.
  Structure, 3, 201-213.
PDB code: 4aa6
  7773178 L.Shimoni, and J.P.Glusker (1995).
Hydrogen bonding motifs of protein side chains: descriptions of binding of arginine and amide groups.
  Protein Sci, 4, 65-74.  
7630723 M.A.Martínez-Balbás, E.Jiménez-García, and F.Azorín (1995).
Zinc(II) ions selectively interact with DNA sequences present at the TFIIIA binding site of the Xenopus 5S-RNA gene.
  Nucleic Acids Res, 23, 2464-2471.  
8749848 M.Suzuki, and M.Gerstein (1995).
Binding geometry of alpha-helices that recognize DNA.
  Proteins, 23, 525-535.  
7610037 M.Suzuki, and N.Yagi (1995).
Stereochemical basis of DNA bending by transcription factors.
  Nucleic Acids Res, 23, 2083-2091.  
7501470 R.P.Hyde-DeRuyscher, E.Jennings, and T.Shenk (1995).
DNA binding sites for the transcriptional activator/repressor YY1.
  Nucleic Acids Res, 23, 4457-4465.  
  7565750 S.Natesan, and M.Gilman (1995).
YY1 facilitates the association of serum response factor with the c-fos serum response element.
  Mol Cell Biol, 15, 5975-5982.  
7862533 T.B.Hamilton, K.C.Barilla, and P.J.Romaniuk (1995).
High affinity binding sites for the Wilms' tumour suppressor protein WT1.
  Nucleic Acids Res, 23, 277-284.  
7579654 Y.Choo, and A.Klug (1995).
Designing DNA-binding proteins on the surface of filamentous phage.
  Curr Opin Biotechnol, 6, 431-436.  
9383408 Y.Shi, and J.M.Berg (1995).
A direct comparison of the properties of natural and designed zinc-finger proteins.
  Chem Biol, 2, 83-89.  
7991626 A.V.Hine, and C.C.Richardson (1994).
A functional chimeric DNA primase: the Cys4 zinc-binding domain of bacteriophage T3 primase fused to the helicase of bacteriophage T7.
  Proc Natl Acad Sci U S A, 91, 12327-12331.  
  8196627 C.Cheng, N.Kacherovsky, K.M.Dombek, S.Camier, S.K.Thukral, E.Rhim, and E.T.Young (1994).
Identification of potential target genes for Adr1p through characterization of essential nucleotides in UAS1.
  Mol Cell Biol, 14, 3842-3852.  
9383374 D.A.Erlanson, and G.L.Verdine (1994).
Falling out of the fold: tumorigenic mutations and p53.
  Chem Biol, 1, 79-84.  
  8196623 I.A.Drummond, H.D.Rupprecht, P.Rohwer-Nutter, J.M.Lopez-Guisa, S.L.Madden, F.J.Rauscher, and V.P.Sukhatme (1994).
DNA recognition by splicing variants of the Wilms' tumor suppressor, WT1.
  Mol Cell Biol, 14, 3800-3809.  
7664042 J.W.Schwabe, and A.Klug (1994).
Zinc mining for protein domains.
  Nat Struct Biol, 1, 345-349.  
7954830 K.Ogata, S.Morikawa, H.Nakamura, A.Sekikawa, T.Inoue, H.Kanai, A.Sarai, S.Ishii, and Y.Nishimura (1994).
Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices.
  Cell, 79, 639-648.
PDB codes: 1mse 1msf
8041727 L.Nekludova, and C.O.Pabo (1994).
Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes.
  Proc Natl Acad Sci U S A, 91, 6948-6952.  
  8062827 L.von Kalm, K.Crossgrove, D.Von Seggern, G.M.Guild, and S.K.Beckendorf (1994).
The Broad-Complex directly controls a tissue-specific response to the steroid hormone ecdysone at the onset of Drosophila metamorphosis.
  EMBO J, 13, 3505-3516.  
8078776 M.Suzuki, M.Gerstein, and N.Yagi (1994).
Stereochemical basis of DNA recognition by Zn fingers.
  Nucleic Acids Res, 22, 3397-3405.  
7809040 M.Suzuki, and N.Yagi (1994).
DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families.
  Proc Natl Acad Sci U S A, 91, 12357-12361.  
8087558 M.Suzuki (1994).
A framework for the DNA-protein recognition code of the probe helix in transcription factors: the chemical and stereochemical rules.
  Structure, 2, 317-326.  
  8035792 N.Koyano-Nakagawa, J.Nishida, D.Baldwin, K.Arai, and T.Yokota (1994).
Molecular cloning of a novel human cDNA encoding a zinc finger protein that binds to the interleukin-3 promoter.
  Mol Cell Biol, 14, 5099-5107.  
7531280 T.Pieler, and E.Bellefroid (1994).
Perspectives on zinc finger protein function and evolution--an update.
  Mol Biol Rep, 20, 1-8.  
8001572 U.Schäfer, O.Rausch, T.Bouwmeester, and T.Pieler (1994).
Sequence-specific recognition of a repetitive DNA element by a C2H2 zinc-finger protein in Xenopus.
  Eur J Biochem, 226, 567-576.  
7972027 Y.Choo, and A.Klug (1994).
Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage.
  Proc Natl Acad Sci U S A, 91, 11163-11167.  
7972028 Y.Choo, and A.Klug (1994).
Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions.
  Proc Natl Acad Sci U S A, 91, 11168-11172.  
15335830 A.A.Travers, and J.W.Schwabe (1993).
Spurring on transcription?
  Curr Biol, 3, 898-900.  
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.

 

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