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PDBsum entry 1vto
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protein dna_rna Protein-protein interface(s) links
Transcription/DNA PDB id
1vto

 

 

 

 

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Contents
Protein chains
187 a.a.
DNA/RNA
Waters ×1561
PDB id:
1vto
Name: Transcription/DNA
Title: 1.9 a resolution refined structure of tbp recognizing the minor groove of tataaaag
Structure: DNA (5'-d( Gp Cp Tp Ap Tp Ap Ap Ap Ap Gp Gp Gp Cp A)-3'). Chain: c, e. Engineered: yes. DNA (5'-d( Tp Gp Cp Cp Cp Tp Tp Tp Tp Ap Tp Ap Gp C)-3'). Chain: d, f. Engineered: yes. Tata binding protein. Chain: a, b. Synonym: transcription initiation factor tfiid-1, tata-box factor 1,
Source: Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Arabidopsis thaliana. Mouse-ear cress. Organism_taxid: 3702
Resolution:
1.90Å     R-factor:   0.194     R-free:   0.264
Authors: J.L.Kim,S.K.Burley
Key ref: J.L.Kim and S.K.Burley (1994). 1.9 A resolution refined structure of TBP recognizing the minor groove of TATAAAAG. Nat Struct Biol, 1, 638-653. PubMed id: 7634103
Date:
06-Sep-96     Release date:   13-Jul-11    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P28147  (TBP1_ARATH) -  TATA-box-binding protein 1 from Arabidopsis thaliana
Seq:
Struc: 		200 a.a.
187 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  G-C-T-A-T-A-A-A-A-G-G-G-C-A 14 bases
  T-G-C-C-C-T-T-T-T-A-T-A-G-C 14 bases
  G-C-T-A-T-A-A-A-A-G-G-G-C-A 14 bases
  T-G-C-C-C-T-T-T-T-A-T-A-G-C 14 bases

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

 

 
Nat Struct Biol 1:638-653 (1994)
PubMed id: 7634103  
 
 
1.9 A resolution refined structure of TBP recognizing the minor groove of TATAAAAG.
J.L.Kim, S.K.Burley.
 
  ABSTRACT  
 
The three-dimensional structure of a TATA box-binding protein (TBP) from Arabidopsis thaliana complexed with a fourteen base pair oligonucleotide bearing the Adenovirus major late promoter TATA element has been refined at 1.9 A resolution, giving a final crystallographic R-factor of 19.4%. Binding of the monomeric, saddle-shaped alpha/beta protein induces an unprecedented conformational change in the DNA. A detailed structural and functional analysis of this unusual protein-DNA complex is presented, with particular emphasis on the mechanisms of DNA deformation, TATA element recognition, and preinitiation complex assembly.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
16495225 M.Su, D.Lee, B.Ganss, and J.Sodek (2006).
Stereochemical analysis of the functional significance of the conserved inverted CCAAT and TATA elements in the rat bone sialoprotein gene promoter.
  J Biol Chem, 281, 9882-9890.  
14534318 C.A.Adams, S.R.Kar, J.E.Hopper, and M.G.Fried (2004).
Self-association of the amino-terminal domain of the yeast TATA-binding protein.
  J Biol Chem, 279, 1376-1382.  
14660650 M.L.Grace, M.B.Chandrasekharan, T.C.Hall, and A.J.Crowe (2004).
Sequence and spacing of TATA box elements are critical for accurate initiation from the beta-phaseolin promoter.
  J Biol Chem, 279, 8102-8110.  
11863454 A.R.Kays, and A.Schepartz (2002).
Gal4-VP16 and Gal4-AH increase the orientational and axial specificity of TATA box recognition by TATA box binding protein.
  Biochemistry, 41, 3147-3155.  
11726667 R.M.Powell, K.M.Parkhurst, and L.J.Parkhurst (2002).
Comparison of TATA-binding protein recognition of a variant and consensus DNA promoters.
  J Biol Chem, 277, 7776-7784.  
11564744 P.Cabart, and S.Murphy (2001).
BRFU, a TFIIB-like factor, is directly recruited to the TATA-box of polymerase III small nuclear RNA gene promoters through its interaction with TATA-binding protein.
  J Biol Chem, 276, 43056-43064.  
10736150 J.D.Kahn (2000).
Topological effects of the TATA box binding protein on minicircle DNA and a possible thermodynamic linkage to chromatin remodeling.
  Biochemistry, 39, 3520-3524.  
10642178 J.M.Benevides, G.Chan, X.J.Lu, W.K.Olson, M.A.Weiss, and G.J.Thomas (2000).
Protein-directed DNA structure. I. Raman spectroscopy of a high-mobility-group box with application to human sex reversal.
  Biochemistry, 39, 537-547.  
10617643 L.P.Perera (2000).
The TATA motif specifies the differential activation of minimal promoters by varicella zoster virus immediate-early regulatory protein IE62.
  J Biol Chem, 275, 487-496.  
10769145 M.A.Daugherty, M.Brenowitz, and M.G.Fried (2000).
Participation of the amino-terminal domain in the self-association of the full-length yeast TATA binding protein.
  Biochemistry, 39, 4869-4880.  
10391913 Y.Xia, and B.E.Uhlin (1999).
Mutational analysis of the PapB transcriptional regulator in Escherichia coli. Regions important for DNA binding and oligomerization.
  J Biol Chem, 274, 19723-19730.  
9628480 D.N.Arvidson, F.Lu, C.Faber, H.Zalkin, and R.G.Brennan (1998).
The structure of PurR mutant L54M shows an alternative route to DNA kinking.
  Nat Struct Biol, 5, 436-441.
PDB code: 1vpw
9468512 M.D.Librizzi, M.Brenowitz, and I.M.Willis (1998).
The TATA element and its context affect the cooperative interaction of TATA-binding protein with the TFIIB-related factor, TFIIIB70.
  J Biol Chem, 273, 4563-4568.  
9843390 V.Petri, M.Hsieh, E.Jamison, and M.Brenowitz (1998).
DNA sequence-specific recognition by the Saccharomyces cerevisiae "TATA" binding protein: promoter-dependent differences in the thermodynamics and kinetics of binding.
  Biochemistry, 37, 15842-15849.  
8688420 M.R.Kurpiewski, M.Koziolkiewicz, A.Wilk, W.J.Stec, and L.Jen-Jacobson (1996).
Chiral phosphorothioates as probes of protein interactions with individual DNA phosphoryl oxygens: essential interactions of EcoRI endonuclease with the phosphate at pGAATTC.
  Biochemistry, 35, 8846-8854.  
7775442 R.A.Coleman, A.K.Taggart, L.R.Benjamin, and B.F.Pugh (1995).
Dimerization of the TATA binding protein.
  J Biol Chem, 270, 13842-13849.  
7775443 R.A.Coleman, and B.F.Pugh (1995).
Evidence for functional binding and stable sliding of the TATA binding protein on nonspecific DNA.
  J Biol Chem, 270, 13850-13859.  
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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