 |
PDBsum entry 2asb
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Transcription/RNA
|
PDB id
|
|
|
|
2asb
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
EMBO J
24:3576-3587
(2005)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Structure of a Mycobacterium tuberculosis NusA-RNA complex.
|
|
B.Beuth,
S.Pennell,
K.B.Arnvig,
S.R.Martin,
I.A.Taylor.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
NusA is a key regulator of bacterial transcriptional elongation, pausing,
termination and antitermination, yet relatively little is known about the
molecular basis of its activity in these fundamental processes. In Mycobacterium
tuberculosis, NusA has been shown to bind with high affinity and specificity to
BoxB-BoxA-BoxC antitermination sequences within the leader region of the single
ribosomal RNA (rRNA) operon. We have determined high-resolution X-ray structures
of a complex of NusA with two short oligo-ribonucleotides derived from the BoxC
stem-loop motif and have characterised the interaction of NusA with a variety of
RNAs derived from the antitermination region. These structures reveal the RNA
bound in an extended conformation to a large interacting surface on both KH
domains. Combining structural data with observed spectral and calorimetric
changes, we now show that NusA binding destabilises secondary structure within
rRNA antitermination sequences and propose a model where NusA functions as a
chaperone for nascently forming RNA structures.
|
|
|
|
|
|
| |
Selected figure(s)
|
|
|
|
| |
|
|
|
|
|
|
Figure 5.
Figure 5 A schematic representation of the RNA-protein contacts
in the NusA  Nt-RNA11
complex. Bases represented in grey circles are stacked and
hydrogen bonding interactions coloured red are mediated through
backbone-base contacts.
|
|
Figure 6.
Figure 6 Details of the interaction of the KH domains with
RNA11. (A) Interaction of KH1 with nucleotides Ade42 to Ura46 in
the  /
 groove
of helices 2,
3
and 1-
3
of the KH1 domain. (B) A view highlighting the protein-nucleic
acid interactions around Ade44 and Ade45. The protein is shown
as a green ribbon. The hydrogen bonds of Ade44 to the backbone
are shown together with the interactions of the 2'-hydroxy group
of Ade45. (C) Stereo view of the interactions of Ade50, Ura51
and Ade52 with the protein. The path of the RNA along the groove
of '2/
'3
and '3
in KH2 is shown. (D) Highlights of the network of polar
interactions around Ade50 to Ade52. The protein and RNA are
represented as in panel B.
|
|
|
|
|
|
| |
The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
EMBO J
(2005,
24,
3576-3587)
copyright 2005.
|
|
| |
Figures were
selected
by the author.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
F.Werner,
and
D.Grohmann
(2011).
Evolution of multisubunit RNA polymerases in the three domains of life.
|
| |
Nat Rev Microbiol,
9,
85-98.
|
|
|
|
|
|
|
J.P.Mackay,
J.Font,
and
D.J.Segal
(2011).
The prospects for designer single-stranded RNA-binding proteins.
|
| |
Nat Struct Mol Biol,
18,
256-261.
|
|
|
|
|
|
|
I.Díaz-Moreno,
D.Hollingworth,
G.Kelly,
S.Martin,
M.García-Mayoral,
P.Briata,
R.Gherzi,
and
A.Ramos
(2010).
Orientation of the central domains of KSRP and its implications for the interaction with the RNA targets.
|
| |
Nucleic Acids Res,
38,
5193-5205.
|
|
|
|
|
|
|
M.Naville,
and
D.Gautheret
(2010).
Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation.
|
| |
Genome Biol,
11,
R97.
|
|
|
|
|
|
|
Y.Matsumoto,
Q.Xu,
S.Miyazaki,
C.Kaito,
C.L.Farr,
H.L.Axelrod,
H.J.Chiu,
H.E.Klock,
M.W.Knuth,
M.D.Miller,
M.A.Elsliger,
A.M.Deacon,
A.Godzik,
S.A.Lesley,
K.Sekimizu,
and
I.A.Wilson
(2010).
Structure of a virulence regulatory factor CvfB reveals a novel winged helix RNA binding module.
|
| |
Structure,
18,
537-547.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.R.Kinjo,
and
H.Nakamura
(2009).
Comprehensive structural classification of ligand-binding motifs in proteins.
|
| |
Structure,
17,
234-246.
|
|
|
|
|
|
|
C.Tu,
X.Zhou,
J.E.Tropea,
B.P.Austin,
D.S.Waugh,
D.L.Court,
and
X.Ji
(2009).
Structure of ERA in complex with the 3' end of 16S rRNA: implications for ribosome biogenesis.
|
| |
Proc Natl Acad Sci U S A,
106,
14843-14848.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
I.Díaz-Moreno,
D.Hollingworth,
T.A.Frenkiel,
G.Kelly,
S.Martin,
S.Howell,
M.García-Mayoral,
R.Gherzi,
P.Briata,
and
A.Ramos
(2009).
Phosphorylation-mediated unfolding of a KH domain regulates KSRP localization via 14-3-3 binding.
|
| |
Nat Struct Mol Biol,
16,
238-246.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.Mercante,
A.N.Edwards,
A.K.Dubey,
P.Babitzke,
and
T.Romeo
(2009).
Molecular geometry of CsrA (RsmA) binding to RNA and its implications for regulated expression.
|
| |
J Mol Biol,
392,
511-528.
|
|
|
|
|
|
|
S.Prasch,
M.Jurk,
R.S.Washburn,
M.E.Gottesman,
B.M.Wöhrl,
and
P.Rösch
(2009).
RNA-binding specificity of E. coli NusA.
|
| |
Nucleic Acids Res,
37,
4736-4742.
|
|
|
|
|
|
|
X.Yang,
S.Molimau,
G.P.Doherty,
E.B.Johnston,
J.Marles-Wright,
R.Rothnagel,
B.Hankamer,
R.J.Lewis,
and
P.J.Lewis
(2009).
The structure of bacterial RNA polymerase in complex with the essential transcription elongation factor NusA.
|
| |
EMBO Rep,
10,
997.
|
|
|
|
|
|
|
J.W.Roberts,
S.Shankar,
and
J.J.Filter
(2008).
RNA polymerase elongation factors.
|
| |
Annu Rev Microbiol,
62,
211-233.
|
|
|
|
|
|
|
K.B.Arnvig,
S.Zeng,
S.Quan,
A.Papageorge,
N.Zhang,
A.C.Villapakkam,
and
C.L.Squires
(2008).
Evolutionary comparison of ribosomal operon antitermination function.
|
| |
J Bacteriol,
190,
7251-7257.
|
|
|
|
|
|
|
R.Valverde,
L.Edwards,
and
L.Regan
(2008).
Structure and function of KH domains.
|
| |
FEBS J,
275,
2712-2726.
|
|
|
|
|
|
|
X.Luo,
H.H.Hsiao,
M.Bubunenko,
G.Weber,
D.L.Court,
M.E.Gottesman,
H.Urlaub,
and
M.C.Wahl
(2008).
Structural and functional analysis of the E. coli NusB-S10 transcription antitermination complex.
|
| |
Mol Cell,
32,
791-802.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
B.M.Lunde,
C.Moore,
and
G.Varani
(2007).
RNA-binding proteins: modular design for efficient function.
|
| |
Nat Rev Mol Cell Biol,
8,
479-490.
|
|
|
|
|
|
|
F.Werner
(2007).
Structure and function of archaeal RNA polymerases.
|
| |
Mol Microbiol,
65,
1395-1404.
|
|
|
|
|
|
|
L.M.Wadley,
K.S.Keating,
C.M.Duarte,
and
A.M.Pyle
(2007).
Evaluating and learning from RNA pseudotorsional space: quantitative validation of a reduced representation for RNA structure.
|
| |
J Mol Biol,
372,
942-957.
|
|
|
|
|
|
|
M.F.García-Mayoral,
D.Hollingworth,
L.Masino,
I.Díaz-Moreno,
G.Kelly,
R.Gherzi,
C.F.Chou,
C.Y.Chen,
and
A.Ramos
(2007).
The structure of the C-terminal KH domains of KSRP reveals a noncanonical motif important for mRNA degradation.
|
| |
Structure,
15,
485-498.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
S.Hare,
W.Fischer,
R.Williams,
L.Terradot,
R.Bayliss,
R.Haas,
and
G.Waksman
(2007).
Identification, structure and mode of action of a new regulator of the Helicobacter pylori HP0525 ATPase.
|
| |
EMBO J,
26,
4926-4934.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.D.Auweter,
F.C.Oberstrass,
and
F.H.Allain
(2006).
Sequence-specific binding of single-stranded RNA: is there a code for recognition?
|
| |
Nucleic Acids Res,
34,
4943-4959.
|
|
|
|
|
|
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
