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PDBsum entry 1qn4
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Tata box-binding protein (tbp)
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PDB id
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1qn4
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Contents |
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* Residue conservation analysis
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PDB id:
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| Name: |
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Tata box-binding protein (tbp)
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Title:
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Crystal structure of the t(-24) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). Tata element recognition by the tata box-binding protein has been conserved throughout evolution.
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Structure:
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Transcription initiation factor tfiid-1. Chain: a, b. Synonym: tata-box factor 1, tata sequence-binding protein 1, tbp1. Engineered: yes. DNA (5'-d( Gp Cp Tp Ap Tp Ap Ap Ap Ap Tp Gp Gp Cp A)-3'). Chain: c, e. Engineered: yes. DNA (5'-d( Tp Gp Cp Cp Ap Tp Tp Tp Tp Ap Tp Ap Gp C)-3'). Chain: d, f.
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Source:
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Arabidopsis thaliana. Mouse-ear cress. Organism_taxid: 3702. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes
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Biol. unit:
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Trimer (from
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Resolution:
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1.86Å
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R-factor:
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0.210
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R-free:
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0.264
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Authors:
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G.A.Patikoglou,J.L.Kim,L.Sun,S.-H.Yang,T.Kodadek,S.K.Burley
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Key ref:
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G.A.Patikoglou
et al.
(1999).
TATA element recognition by the TATA box-binding protein has been conserved throughout evolution.
Genes Dev,
13,
3217-3230.
PubMed id:
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Date:
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14-Oct-99
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Release date:
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06-Feb-00
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PROCHECK
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Headers
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References
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P28147
(TBP1_ARATH) -
TATA-box-binding protein 1 from Arabidopsis thaliana
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Seq:
Struc:
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200 a.a.
183 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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G-C-T-A-T-A-A-A-A-T-G-G-C-A
14 bases
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T-G-C-C-A-T-T-T-T-A-T-A-G-C
14 bases
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G-C-T-A-T-A-A-A-A-T-G-G-C-A
14 bases
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T-G-C-C-A-T-T-T-T-A-T-A-G-C
14 bases
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Genes Dev
13:3217-3230
(1999)
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PubMed id:
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TATA element recognition by the TATA box-binding protein has been conserved throughout evolution.
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G.A.Patikoglou,
J.L.Kim,
L.Sun,
S.H.Yang,
T.Kodadek,
S.K.Burley.
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ABSTRACT
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Cocrystal structures of wild-type TATA box-binding protein (TBP) recognizing 10
naturally occurring TATA elements have been determined at 2.3-1.8 A resolution,
and compared with our 1.9 A resolution structure of TBP bound to the Adenovirus
major late promoter (AdMLP) TATA box (5'-TATAAAAG-3'). Minor-groove recognition
by the saddle-shaped protein induces the same conformational change in each of
these oligonucleotides, despite variations in promoter sequence that reduce the
efficiency of transcription initiation. Three molecular mechanisms explain
assembly of diverse TBP-TATA element complexes. (1) T --> A and A --> T
transversions leave the minor-groove face unchanged, permitting formation of
TBP-DNA complexes on many A/T-rich core promoter sequences. (2) Cavities in the
interface between TBP and the minor-groove face of the AdMLP TATA box
accommodate the exocyclic NH(2) groups of G in a TACA box and in a TATAAG box.
(3) Formation of a C:G Hoogsteen basepair in a TATAAAC box eliminates steric
clashes that would be produced by the Watson-Crick base pair. We conclude that
the structure of the TBP-TATA box complex found at the heart of the polymerase
II (pol II) transcription machinery has remained constant over the course of
evolution, despite variations in TBP and its DNA targets.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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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.
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J Comput Chem,
32,
416-428.
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E.N.Nikolova,
E.Kim,
A.A.Wise,
P.J.O'Brien,
I.Andricioaei,
and
H.M.Al-Hashimi
(2011).
Transient Hoogsteen base pairs in canonical duplex DNA.
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Nature,
470,
498-502.
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F.Werner,
and
D.Grohmann
(2011).
Evolution of multisubunit RNA polymerases in the three domains of life.
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Nat Rev Microbiol,
9,
85-98.
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K.M.Schlitt,
A.L.Millen,
S.D.Wetmore,
and
R.A.Manderville
(2011).
An indole-linked C8-deoxyguanosine nucleoside acts as a fluorescent reporter of Watson-Crick versus Hoogsteen base pairing.
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Org Biomol Chem,
9,
1565-1571.
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P.Khare,
S.I.Mortimer,
C.L.Cleto,
K.Okamura,
Y.Suzuki,
T.Kusakabe,
K.Nakai,
T.H.Meedel,
and
K.E.Hastings
(2011).
Cross-validated methods for promoter/transcription start site mapping in SL trans-spliced genes, established using the Ciona intestinalis troponin I gene.
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Nucleic Acids Res,
39,
2638-2648.
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J.Konc,
and
D.Janezic
(2010).
ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment.
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Bioinformatics,
26,
1160-1168.
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M.A.Gérard,
E.Myslinski,
N.Chylak,
S.Baudrey,
A.Krol,
and
P.Carbon
(2010).
The scaRNA2 is produced by an independent transcription unit and its processing is directed by the encoding region.
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Nucleic Acids Res,
38,
370-381.
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M.Kitayner,
H.Rozenberg,
R.Rohs,
O.Suad,
D.Rabinovich,
B.Honig,
and
Z.Shakked
(2010).
Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs.
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Nat Struct Mol Biol,
17,
423-429.
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PDB codes:
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R.Rohs,
X.Jin,
S.M.West,
R.Joshi,
B.Honig,
and
R.S.Mann
(2010).
Origins of specificity in protein-DNA recognition.
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Annu Rev Biochem,
79,
233-269.
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V.Bernard,
A.Lecharny,
and
V.Brunaud
(2010).
Improved detection of motifs with preferential location in promoters.
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Genome,
53,
739-752.
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V.Bernard,
V.Brunaud,
and
A.Lecharny
(2010).
TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation.
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BMC Genomics,
11,
166.
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A.Marathe,
D.Karandur,
and
M.Bansal
(2009).
Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs.
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BMC Struct Biol,
9,
24.
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D.T.Auble
(2009).
The dynamic personality of TATA-binding protein.
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Trends Biochem Sci,
34,
49-52.
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L.K.Savinkova,
M.P.Ponomarenko,
P.M.Ponomarenko,
I.A.Drachkova,
M.V.Lysova,
T.V.Arshinova,
and
N.A.Kolchanov
(2009).
TATA box polymorphisms in human gene promoters and associated hereditary pathologies.
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Biochemistry (Mosc),
74,
117-129.
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N.B.Becker,
and
R.Everaers
(2009).
DNA nanomechanics: how proteins deform the double helix.
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J Chem Phys,
130,
135102.
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R.O.Sprouse,
M.N.Wells,
and
D.T.Auble
(2009).
TATA-binding protein variants that bypass the requirement for Mot1 in vivo.
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J Biol Chem,
284,
4525-4535.
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D.Svozil,
J.Kalina,
M.Omelka,
and
B.Schneider
(2008).
DNA conformations and their sequence preferences.
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Nucleic Acids Res,
36,
3690-3706.
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G.Bjornsdottir,
and
L.C.Myers
(2008).
Minimal components of the RNA polymerase II transcription apparatus determine the consensus TATA box.
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Nucleic Acids Res,
36,
2906-2916.
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J.H.Bredenberg,
C.Russo,
and
M.O.Fenley
(2008).
Salt-mediated electrostatics in the association of TATA binding proteins to DNA: a combined molecular mechanics/Poisson-Boltzmann study.
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Biophys J,
94,
4634-4645.
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J.R.Choudhury,
R.Guddneppanavar,
G.Saluta,
G.L.Kucera,
and
U.Bierbach
(2008).
Tuning the DNA conformational perturbations induced by cytotoxic platinum-acridine bisintercalators: effect of metal cis/trans isomerism and DNA threading groups.
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J Med Chem,
51,
3069-3072.
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K.L.Whiteson,
and
P.A.Rice
(2008).
Binding and catalytic contributions to site recognition by flp recombinase.
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J Biol Chem,
283,
11414-11423.
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R.Mehta,
V.Sundaravaradan,
and
N.Ahmad
(2008).
Mutations generated in human immunodeficiency virus type 1 long terminal repeat during vertical transmission correlate with viral gene expression.
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Virology,
375,
170-181.
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R.O.Sprouse,
I.Shcherbakova,
H.Cheng,
E.Jamison,
M.Brenowitz,
and
D.T.Auble
(2008).
Function and structural organization of Mot1 bound to a natural target promoter.
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J Biol Chem,
283,
24935-24948.
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R.O.Sprouse,
T.S.Karpova,
F.Mueller,
A.Dasgupta,
J.G.McNally,
and
D.T.Auble
(2008).
Regulation of TATA-binding protein dynamics in living yeast cells.
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Proc Natl Acad Sci U S A,
105,
13304-13308.
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R.Rajesh,
and
K.C.Majumdar
(2008).
The growth hormone-encoding gene isolated and characterized from Labeo rohita Hamilton is expressed in CHO cells under the control of constitutive promoters in 'autotransgene' constructs.
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Fish Physiol Biochem,
34,
413-436.
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C.L.Bassett,
A.M.Callahan,
T.S.Artlip,
R.Scorza,
and
C.Srinivasan
(2007).
A minimal peach type II chlorophyll a/b-binding protein promoter retains tissue-specificity and light regulation in tomato.
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BMC Biotechnol,
7,
47.
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C.Yang,
E.Bolotin,
T.Jiang,
F.M.Sladek,
and
E.Martinez
(2007).
Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters.
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Gene,
389,
52-65.
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H.Faiger,
M.Ivanchenko,
and
T.E.Haran
(2007).
Nearest-neighbor non-additivity versus long-range non-additivity in TATA-box structure and its implications for TBP-binding mechanism.
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Nucleic Acids Res,
35,
4409-4419.
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I.Skovorodkin,
A.Pimenov,
I.Raykhel,
B.Schimanski,
D.Ammermann,
and
A.Günzl
(2007).
alpha-tubulin minichromosome promoters in the stichotrichous ciliate Stylonychia lemnae.
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Eukaryot Cell,
6,
28-36.
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M.F.Lukacs,
H.Harstad,
U.Grimholt,
M.Beetz-Sargent,
G.A.Cooper,
L.Reid,
H.G.Bakke,
R.B.Phillips,
K.M.Miller,
W.S.Davidson,
and
B.F.Koop
(2007).
Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon (Salmo salar).
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BMC Genomics,
8,
251.
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M.J.Hannon
(2007).
Supramolecular DNA recognition.
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Chem Soc Rev,
36,
280-295.
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S.Khrapunov,
and
M.Brenowitz
(2007).
Influence of the N-terminal domain and divalent cations on self-association and DNA binding by the Saccharomyces cerevisiae TATA binding protein.
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Biochemistry,
46,
4876-4887.
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T.A.Robertson,
and
G.Varani
(2007).
An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure.
|
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Proteins,
66,
359-374.
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E.Cubero,
F.J.Luque,
and
M.Orozco
(2006).
Theoretical study of the Hoogsteen-Watson-Crick junctions in DNA.
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Biophys J,
90,
1000-1008.
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H.Faiger,
M.Ivanchenko,
I.Cohen,
and
T.E.Haran
(2006).
TBP flanking sequences: asymmetry of binding, long-range effects and consensus sequences.
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Nucleic Acids Res,
34,
104-119.
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I.Shcherbakova,
S.Mitra,
R.H.Beer,
and
M.Brenowitz
(2006).
Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins.
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Nucleic Acids Res,
34,
e48.
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I.Tirosh,
A.Weinberger,
M.Carmi,
and
N.Barkai
(2006).
A genetic signature of interspecies variations in gene expression.
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Nat Genet,
38,
830-834.
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I.Wierstra,
and
J.Alves
(2006).
FOXM1c transactivates the human c-myc promoter directly via the two TATA boxes P1 and P2.
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FEBS J,
273,
4645-4667.
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N.D.Tsihlis,
and
A.Grove
(2006).
The Saccharomyces cerevisiae RNA polymerase III recruitment factor subunits Brf1 and Bdp1 impose a strict sequence preference for the downstream half of the TATA box.
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Nucleic Acids Res,
34,
5585-5593.
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Q.Zhang,
and
T.Schlick
(2006).
Stereochemistry and position-dependent effects of carcinogens on TATA/TBP binding.
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Biophys J,
90,
1865-1877.
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S.L.Williams,
L.K.Parkhurst,
and
L.J.Parkhurst
(2006).
Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer.
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| |
Nucleic Acids Res,
34,
1028-1035.
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G.de Dios-Bravo,
J.P.Luna-Arias,
A.M.Riverón,
J.J.Olivares-Trejo,
C.López-Camarillo,
and
E.Orozco
(2005).
Entamoeba histolytica TATA-box binding protein binds to different TATA variants in vitro.
|
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FEBS J,
272,
1354-1366.
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J.R.Choudhury,
and
U.Bierbach
(2005).
Characterization of the bisintercalative DNA binding mode of a bifunctional platinum-acridine agent.
|
| |
Nucleic Acids Res,
33,
5622-5632.
|
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K.Florquin,
Y.Saeys,
S.Degroeve,
P.Rouzé,
and
Y.Van de Peer
(2005).
Large-scale structural analysis of the core promoter in mammalian and plant genomes.
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| |
Nucleic Acids Res,
33,
4255-4264.
|
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R.P.Perry
(2005).
The architecture of mammalian ribosomal protein promoters.
|
| |
BMC Evol Biol,
5,
15.
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G.Paillard,
and
R.Lavery
(2004).
Analyzing protein-DNA recognition mechanisms.
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Structure,
12,
113-122.
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H.T.Chen,
and
S.Hahn
(2004).
Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex: a model for the structure of the PIC.
|
| |
Cell,
119,
169-180.
|
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N.Adachi,
R.Natsume,
M.Senda,
S.Muto,
T.Senda,
and
M.Horikoshi
(2004).
Purification, crystallization and preliminary X-ray analysis of Methanococcus jannaschii TATA box-binding protein (TBP).
|
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Acta Crystallogr D Biol Crystallogr,
60,
2328-2331.
|
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|
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S.Hahn
(2004).
Structure and mechanism of the RNA polymerase II transcription machinery.
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Nat Struct Mol Biol,
11,
394-403.
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T.van Opijnen,
J.Kamoschinski,
R.E.Jeeninga,
and
B.Berkhout
(2004).
The human immunodeficiency virus type 1 promoter contains a CATA box instead of a TATA box for optimal transcription and replication.
|
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J Virol,
78,
6883-6890.
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A.K.Mishra,
P.Vanathi,
and
P.Bhargava
(2003).
The transcriptional activator GAL4-VP16 regulates the intra-molecular interactions of the TATA-binding protein.
|
| |
J Biosci,
28,
423-436.
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D.Strahs,
D.Barash,
X.Qian,
and
T.Schlick
(2003).
Sequence-dependent solution structure and motions of 13 TATA/TBP (TATA-box binding protein) complexes.
|
| |
Biopolymers,
69,
216-243.
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H.Ling,
F.Boudsocq,
B.S.Plosky,
R.Woodgate,
and
W.Yang
(2003).
Replication of a cis-syn thymine dimer at atomic resolution.
|
| |
Nature,
424,
1083-1087.
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PDB codes:
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I.Topalidou,
M.Papamichos-Chronakis,
and
G.Thireos
(2003).
Post-TATA binding protein recruitment clearance of Gcn5-dependent histone acetylation within promoter nucleosomes.
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| |
Mol Cell Biol,
23,
7809-7817.
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M.Labrador,
and
V.G.Corces
(2003).
Phosphorylation of histone H3 during transcriptional activation depends on promoter structure.
|
| |
Genes Dev,
17,
43-48.
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S.Jones,
H.P.Shanahan,
H.M.Berman,
and
J.M.Thornton
(2003).
Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.
|
| |
Nucleic Acids Res,
31,
7189-7198.
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S.T.Smale,
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PDB code:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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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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