 |
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
Enzyme class:
|
|
E.C.2.7.7.6
- DNA-directed Rna polymerase.
|
|
|
|
|
|
|
Reaction:
|
|
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
|
|
|
|
|
|
Nucleoside triphosphate
|
+
|
RNA(n)
|
=
|
diphosphate
|
+
|
RNA(n+1)
|
|
|
|
|
|
|
|
|
|
|
|
|
Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
|
|
|
|
|
|
|
|
|
|
|
Gene Ontology (GO) functional annotation
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Biological process
|
DNA repair
|
2 terms
|
|
|
Biochemical function
|
DNA binding
|
2 terms
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
| |
|
DOI no:
|
J Biol Chem
275:16057-16063
(2000)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
The structure and the characteristic DNA binding property of the C-terminal domain of the RNA polymerase alpha subunit from Thermus thermophilus.
|
|
T.Wada,
T.Yamazaki,
Y.Kyogoku.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The C-terminal domain of the alpha subunit of the RNA polymerase (alphaCTD) from
Escherichia coli (Ec) regulates transcription by interacting with many kinds of
proteins and promoter upstream (UP) elements consisting of AT-rich sequences.
However, it is unclear how this system is common in all eubacteria. We
investigate the structure and properties of alphaCTD from an extremely
thermophilic eubacterium, Thermus thermophilus (Tt). The solution structure of
Tt alphaCTD (85 amino acids) was determined by NMR, and the interaction between
Tt alphaCTD and DNA with different sequences was investigated by means of
chemical shift perturbation experiments. The tertiary structure of Tt alphaCTD
is almost identical with that of Ec alphaCTD despite 32% sequence homology.
However, Tt alphaCTD interacts with the upstream region sequence of the promoter
in the Tt 16 S ribosomal protein operon rather than the Ec UP element DNA. The
upstream region sequence of Tt is composed of 25 base pairs with 40% AT, unlike
the Ec UP element with 80% AT. The DNA binding site in Tt alphaCTD is located on
the surface composed of helix 4 and the loop preceding helix 4. The electric
charges on this surface are not remarkably localized like those of Ec alphaCTD.
|
|
|
|
|
|
| |
Selected figure(s)
|
|
|
|
| |
|
|
|
|
|
|
Figure 6.
Fig. 6. A, comparison of the backbone of Tt  CTD with
that of Ec CTD. The
backbones of Tt and Ec CTDs are
given as a blue ribbon and red ribbon, respectively. The side
chains of residues Phe^249, Trp321, and Ile^326 in Ec CTD form
the hydrophobic core (6). B, a ribbon representation of the
human BAF monomer ( 26). The green ribbons indicate the five
helices
(H1-H5).
|
|
Figure 7.
Fig. 7. Molecular surfaces of (A) Ec CTD and (B)
Tt CTD. The
molecular surfaces are colored according to the electrostatic
potential; blue corresponds to a positive potential and red to a
negative potential. Residues whose amide resonances were
perturbed by the presence of DNA are connected by green lines
(Ref. 6 and this study). Residues in Ec CTD
connected by yellow lines are important for the interaction with
the UP element in Ec CTD
indicated by the Ala scan experiment (7). Residues Arg265 and
Lys297 in Ec CTD
correspond to Arg264 and Glu296 in Tt CTD,
respectively, whose positions are shown in B. Their surfaces are
viewed from the left side of the view shown in Fig. 4. These
figures were calculated using the GRASP program (33).
|
|
|
|
|
|
| |
The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2000,
275,
16057-16063)
copyright 2000.
|
|
| |
Figures were
selected
by an automated process.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
N.Barinova,
K.Kuznedelov,
K.Severinov,
and
A.Kulbachinskiy
(2008).
Structural modules of RNA polymerase required for transcription from promoters containing downstream basal promoter element GGGA.
|
| |
J Biol Chem, 283,
22482-22489.
|
|
|
|
|
|
|
K.J.Newberry,
S.Nakano,
P.Zuber,
and
R.G.Brennan
(2005).
Crystal structure of the Bacillus subtilis anti-alpha, global transcriptional regulator, Spx, in complex with the alpha C-terminal domain of RNA polymerase.
|
| |
Proc Natl Acad Sci U S A, 102,
15839-15844.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.T.Marr,
J.W.Roberts,
S.E.Brown,
M.Klee,
and
G.N.Gussin
(2004).
Interactions among CII protein, RNA polymerase and the lambda PRE promoter: contacts between RNA polymerase and the -35 region of PRE are identical in the presence and absence of CII protein.
|
| |
Nucleic Acids Res, 32,
1083-1090.
|
|
|
|
|
|
|
W.Ross,
D.A.Schneider,
B.J.Paul,
A.Mertens,
and
R.L.Gourse
(2003).
An intersubunit contact stimulating transcription initiation by E coli RNA polymerase: interaction of the alpha C-terminal domain and sigma region 4.
|
| |
Genes Dev, 17,
1293-1307.
|
|
|
|
|
|
|
S.Singh,
G.E.Folkers,
A.M.Bonvin,
R.Boelens,
R.Wechselberger,
A.Niztayev,
and
R.Kaptein
(2002).
Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli.
|
| |
EMBO J, 21,
6257-6266.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
O.N.Ozoline,
N.Fujita,
and
A.Ishihama
(2001).
Mode of DNA-protein interaction between the C-terminal domain of Escherichia coli RNA polymerase alpha subunit and T7D promoter UP element.
|
| |
Nucleic Acids Res, 29,
4909-4919.
|
|
|
|
|
|
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.
|
|
Links
