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PDBsum entry 1tf3

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protein dna_rna metals links
Transcription/DNA PDB id
1tf3
Jmol
Contents
Protein chain
92 a.a. *
DNA/RNA
Metals
_ZN ×3
* Residue conservation analysis
PDB id:
1tf3
Name: Transcription/DNA
Title: Tfiiia finger 1-3 bound to DNA, nmr, 22 structures
Structure: 5s RNA gene. Chain: e. Fragment: c-block, nt 79-93 of 5s RNA gene, non-coding and coding strands. Synonym: 5s gene. Engineered: yes. 5s RNA gene. Chain: f. Fragment: c-block, nt 79-93 of 5s RNA gene, non-coding and
Source: Synthetic: yes. Other_details: gene fragment encoding fingers 1-3 of tfiiia was subcloned into pet21a plasmid and expressed in escherichia coli bl21 (de3) cells. DNA oligonucleotide was obtained by solid-phase synthesis. Xenopus laevis. African clawed frog. Organism_taxid: 8355. Cell_line: bl21.
NMR struc: 22 models
Authors: M.P.Foster,D.S.Wuttke,I.Radhakrishnan,D.A.Case, J.M.Gottesfeld,P.E.Wright
Key ref: M.P.Foster et al. (1997). Domain packing and dynamics in the DNA complex of the N-terminal zinc fingers of TFIIIA. Nat Struct Biol, 4, 605-608. PubMed id: 9253405
Date:
01-Jul-97     Release date:   17-Sep-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03001  (TF3A_XENLA) -  Transcription factor IIIA
Seq:
Struc:
366 a.a.
92 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

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

 

 
Nat Struct Biol 4:605-608 (1997)
PubMed id: 9253405  
 
 
Domain packing and dynamics in the DNA complex of the N-terminal zinc fingers of TFIIIA.
M.P.Foster, D.S.Wuttke, I.Radhakrishnan, D.A.Case, J.M.Gottesfeld, P.E.Wright.
 
  ABSTRACT  
 
The three N-terminal zinc fingers of transcription factor IIIA bind in the DNA major groove. Substantial packing interfaces are formed between adjacent fingers, the linkers lose their intrinsic flexibility upon DNA binding, and several lysine side chains implicated in DNA recognition are dynamically disordered.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20167128 M.Hatayama, and J.Aruga (2010).
Characterization of the tandem CWCH2 sequence motif: a hallmark of inter-zinc finger interactions.
  BMC Evol Biol, 10, 53.  
19179334 D.F.Estrada, D.M.Boudreaux, D.Zhong, S.C.St Jeor, and R.N.De Guzman (2009).
The Hantavirus Glycoprotein G1 Tail Contains Dual CCHC-type Classical Zinc Fingers.
  J Biol Chem, 284, 8654-8660.
PDB code: 2k9h
19105660 N.Trbovic, J.H.Cho, R.Abel, R.A.Friesner, M.Rance, and A.G.Palmer (2009).
Protein side-chain dynamics and residual conformational entropy.
  J Am Chem Soc, 131, 615-622.  
19119423 R.O.Emerson, and J.H.Thomas (2009).
Adaptive evolution in zinc finger transcription factors.
  PLoS Genet, 5, e1000325.  
17452323 E.López-Viñas, A.Bentebibel, C.Gurunathan, M.Morillas, D.de Arriaga, D.Serra, G.Asins, F.G.Hegardt, and P.Gómez-Puertas (2007).
Definition by functional and structural analysis of two malonyl-CoA sites in carnitine palmitoyltransferase 1A.
  J Biol Chem, 282, 18212-18224.  
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.  
16385466 D.Lugtenberg, H.G.Yntema, M.J.Banning, A.R.Oudakker, H.V.Firth, L.Willatt, M.Raynaud, T.Kleefstra, J.P.Fryns, H.H.Ropers, J.Chelly, C.Moraine, J.Gecz, J.van Reeuwijk, S.B.Nabuurs, B.B.de Vries, B.C.Hamel, A.P.de Brouwer, and H.van Bokhoven (2006).
ZNF674: a new kruppel-associated box-containing zinc-finger gene involved in nonsyndromic X-linked mental retardation.
  Am J Hum Genet, 78, 265-278.  
16734424 J.Liu, N.B.Perumal, C.J.Oldfield, E.W.Su, V.N.Uversky, and A.K.Dunker (2006).
Intrinsic disorder in transcription factors.
  Biochemistry, 45, 6873-6888.  
16847313 Y.Li, T.Kimura, J.H.Laity, and G.K.Andrews (2006).
The zinc-sensing mechanism of mouse MTF-1 involves linker peptides between the zinc fingers.
  Mol Cell Biol, 26, 5580-5587.  
16055450 B.M.Potter, L.S.Feng, P.Parasuram, V.A.Matskevich, J.A.Wilson, G.K.Andrews, and J.H.Laity (2005).
The six zinc fingers of metal-responsive element binding transcription factor-1 form stable and quasi-ordered structures with relatively small differences in zinc affinities.
  J Biol Chem, 280, 28529-28540.  
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.  
15888446 K.L.Brady, S.N.Ponnampalam, M.J.Bumbulis, and D.R.Setzer (2005).
Mutations in TFIIIA that increase stability of the TFIIIA-5 S rRNA gene complex: unusual effects on the kinetics of complex assembly and dissociation.
  J Biol Chem, 280, 26743-26750.  
15340924 K.B.Murray, W.R.Taylor, and J.M.Thornton (2004).
Toward the detection and validation of repeats in protein structure.
  Proteins, 57, 365-380.  
12657633 C.A.Plambeck, A.H.Kwan, D.J.Adams, B.J.Westman, L.van der Weyden, R.L.Medcalf, B.J.Morris, and J.P.Mackay (2003).
The structure of the zinc finger domain from human splicing factor ZNF265 fold.
  J Biol Chem, 278, 22805-22811.
PDB code: 1n0z
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
12592032 H.B.Kamadurai, S.Subramaniam, R.B.Jones, K.B.Green-Church, and M.P.Foster (2003).
Protein folding coupled to DNA binding in the catalytic domain of bacteriophage lambda integrase detected by mass spectrometry.
  Protein Sci, 12, 620-626.  
12493834 M.Zeeb, and J.Balbach (2003).
Single-stranded DNA binding of the cold-shock protein CspB from Bacillus subtilis: NMR mapping and mutational characterization.
  Protein Sci, 12, 112-123.  
14674754 W.Nomura, and Y.Sugiura (2003).
Effects of length and position of an extended linker on sequence-selective DNA recognition of zinc finger peptides.
  Biochemistry, 42, 14805-14813.  
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.  
11524427 D.P.Giedroc, X.Chen, M.A.Pennella, and A.C.LiWang (2001).
Conformational heterogeneity in the C-terminal zinc fingers of human MTF-1: an NMR and zinc-binding study.
  J Biol Chem, 276, 42322-42332.  
11251291 H.B.Houbaviy, and S.K.Burley (2001).
Thermodynamic analysis of the interaction between YY1 and the AAV P5 promoter initiator element.
  Chem Biol, 8, 179-187.  
11179890 J.H.Laity, B.M.Lee, and P.E.Wright (2001).
Zinc finger proteins: new insights into structural and functional diversity.
  Curr Opin Struct Biol, 11, 39-46.  
11738049 T.Nishikawa, H.Okamura, A.Nagadoi, P.König, D.Rhodes, and Y.Nishimura (2001).
Solution structure of a telomeric DNA complex of human TRF1.
  Structure, 9, 1237-1251.
PDB codes: 1ity 1iv6
11151005 U.Dengler, A.S.Siddiqui, and G.J.Barton (2001).
Protein structural domains: analysis of the 3Dee domains database.
  Proteins, 42, 332-344.  
11050227 J.H.Laity, H.J.Dyson, and P.E.Wright (2000).
Molecular basis for modulation of biological function by alternate splicing of the Wilms' tumor suppressor protein.
  Proc Natl Acad Sci U S A, 97, 11932-11935.  
10684922 M.R.Paule, and R.J.White (2000).
Survey and summary: transcription by RNA polymerases I and III.
  Nucleic Acids Res, 28, 1283-1298.  
10773080 M.Schaub, A.Krol, and P.Carbon (2000).
Structural organization of Staf-DNA complexes.
  Nucleic Acids Res, 28, 2114-2121.  
11000262 P.E.Verdemato, J.A.Brannigan, C.Damblon, F.Zuccotto, P.C.Moody, and L.Y.Lian (2000).
DNA-binding mechanism of the Escherichia coli Ada O(6)-alkylguanine-DNA alkyltransferase.
  Nucleic Acids Res, 28, 3710-3718.  
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.  
10090291 H.Kono, and A.Sarai (1999).
Structure-based prediction of DNA target sites by regulatory proteins.
  Proteins, 35, 114-131.  
9891026 S.Pizzi, G.Dieci, P.Frigeri, G.Piccoli, V.Stocchi, and S.Ottonello (1999).
Domain organization and functional properties of yeast transcription factor IIIA species with different zinc stoichiometries.
  J Biol Chem, 274, 2539-2548.  
10026248 V.Gopalan, H.Kühne, R.Biswas, H.Li, G.W.Brudvig, and S.Altman (1999).
Mapping RNA-protein interactions in ribonuclease P from Escherichia coli using electron paramagnetic resonance spectroscopy.
  Biochemistry, 38, 1705-1714.  
9558357 C.Jin, I.Marsden, X.Chen, and X.Liao (1998).
Sequence specific collective motions in a winged helix DNA binding domain detected by 15N relaxation NMR.
  Biochemistry, 37, 6179-6187.  
9631300 J.A.McCammon (1998).
Theory of biomolecular recognition.
  Curr Opin Struct Biol, 8, 245-249.  
9724513 M.Isalan, A.Klug, and Y.Choo (1998).
Comprehensive DNA recognition through concerted interactions from adjacent zinc fingers.
  Biochemistry, 37, 12026-12033.  
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.  
9430589 R.N.De Guzman, Z.R.Wu, C.C.Stalling, L.Pappalardo, P.N.Borer, and M.F.Summers (1998).
Structure of the HIV-1 nucleocapsid protein bound to the SL3 psi-RNA recognition element.
  Science, 279, 384-388.
PDB code: 1a1t
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
9519295 S.Tan, and T.J.Richmond (1998).
Eukaryotic transcription factors.
  Curr Opin Struct Biol, 8, 41-48.  
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.  
9421515 Y.Choo (1998).
End effects in DNA recognition by zinc finger arrays.
  Nucleic Acids Res, 26, 554-557.  
9287156 Y.Li, and D.H.Turner (1997).
Effects of Mg2+ and the 2' OH of guanosine on steps required for substrate binding and reactivity with the Tetrahymena ribozyme reveal several local folding transitions.
  Biochemistry, 36, 11131-11139.  
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.