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PDBsum entry 1ny6
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Transcription
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PDB id
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1ny6
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Contents |
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* Residue conservation analysis
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PDB id:
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Transcription
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Title:
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Crystal structure of sigm54 activator (aaa+ atpase) in the active state
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Structure:
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Transcriptional regulator (ntrc family). Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n. Fragment: residues 122-387. Engineered: yes
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Source:
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Aquifex aeolicus. Organism_taxid: 63363. Gene: ntrc1. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Biol. unit:
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Heptamer (from
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Resolution:
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3.10Å
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R-factor:
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0.266
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R-free:
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0.329
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Authors:
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S.Y.Lee,A.De La Torre,S.Kustu,B.T.Nixon,D.E.Wemmer
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Key ref:
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S.Y.Lee
et al.
(2003).
Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains.
Genes Dev,
17,
2552-2563.
PubMed id:
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Date:
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11-Feb-03
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Release date:
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11-Nov-03
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PROCHECK
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Headers
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References
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O67198
(O67198_AQUAE) -
Transcriptional regulator (NtrC family) from Aquifex aeolicus (strain VF5)
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Seq:
Struc:
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439 a.a.
247 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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Genes Dev
17:2552-2563
(2003)
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PubMed id:
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Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains.
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S.Y.Lee,
A.De La Torre,
D.Yan,
S.Kustu,
B.T.Nixon,
D.E.Wemmer.
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ABSTRACT
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Transcription by sigma54 RNA polymerase depends on activators that contain
ATPase domains of the AAA+ class. These activators, which are often response
regulators of two-component signal transduction systems, remodel the polymerase
so that it can form open complexes at promoters. Here, we report the first
crystal structures of the ATPase domain of an activator, the NtrC1 protein from
the extreme thermophile Aquifex aeolicus. This domain alone, which is active,
crystallized as a ring-shaped heptamer. The protein carrying both the ATPase and
adjacent receiver domains, which is inactive, crystallized as a dimer. In the
inactive dimer, one residue needed for catalysis is far from the active site,
and extensive contacts among the domains prevent oligomerization of the ATPase
domain. Oligomerization, which completes the active site, depends on surfaces
that are buried in the dimer, and hence, on a rearrangement of the receiver
domains upon phosphorylation. A motif in the ATPase domain known to be critical
for coupling energy to remodeling of polymerase forms a novel loop that projects
from the middle of an alpha helix. The extended, structured loops from the
subunits of the heptamer localize to a pore in the center of the ring and form a
surface that could contact sigma54.
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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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M.Bush,
T.Ghosh,
N.Tucker,
X.Zhang,
and
R.Dixon
(2011).
Transcriptional regulation by the dedicated nitric oxide sensor, NorR: a route towards NO detoxification.
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Biochem Soc Trans,
39,
289-293.
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M.Jovanovic,
E.H.James,
P.C.Burrows,
F.G.Rego,
M.Buck,
and
J.Schumacher
(2011).
Regulation of the co-evolved HrpR and HrpS AAA+ proteins required for Pseudomonas syringae pathogenicity.
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Nat Commun,
2,
177.
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B.Chen,
T.A.Sysoeva,
S.Chowdhury,
L.Guo,
S.De Carlo,
J.A.Hanson,
H.Yang,
and
B.T.Nixon
(2010).
Engagement of arginine finger to ATP triggers large conformational changes in NtrC1 AAA+ ATPase for remodeling bacterial RNA polymerase.
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Structure,
18,
1420-1430.
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PDB code:
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H.J.Sterling,
J.D.Batchelor,
D.E.Wemmer,
and
E.R.Williams
(2010).
Effects of buffer loading for electrospray ionization mass spectrometry of a noncovalent protein complex that requires high concentrations of essential salts.
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J Am Soc Mass Spectrom,
21,
1045-1049.
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M.Buck,
and
T.R.Hoover
(2010).
An ATPase R-finger leaves its print on transcriptional activation.
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Structure,
18,
1391-1392.
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M.Bush,
T.Ghosh,
N.Tucker,
X.Zhang,
and
R.Dixon
(2010).
Nitric oxide-responsive interdomain regulation targets the σ54-interaction surface in the enhancer binding protein NorR.
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Mol Microbiol,
77,
1278-1288.
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M.El Bakkouri,
I.Gutsche,
U.Kanjee,
B.Zhao,
M.Yu,
G.Goret,
G.Schoehn,
W.P.Burmeister,
and
W.A.Houry
(2010).
Structure of RavA MoxR AAA+ protein reveals the design principles of a molecular cage modulating the inducible lysine decarboxylase activity.
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Proc Natl Acad Sci U S A,
107,
22499-22504.
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PDB code:
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P.C.Burrows,
N.Joly,
and
M.Buck
(2010).
A prehydrolysis state of an AAA+ ATPase supports transcription activation of an enhancer-dependent RNA polymerase.
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Proc Natl Acad Sci U S A,
107,
9376-9381.
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R.Gao,
and
A.M.Stock
(2010).
Molecular strategies for phosphorylation-mediated regulation of response regulator activity.
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Curr Opin Microbiol,
13,
160-167.
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S.Sardiwal,
J.M.Santini,
T.H.Osborne,
and
S.Djordjevic
(2010).
Characterization of a two-component signal transduction system that controls arsenite oxidation in the chemolithoautotroph NT-26.
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FEMS Microbiol Lett,
313,
20-28.
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T.R.Sweeney,
V.Cisnetto,
D.Bose,
M.Bailey,
J.R.Wilson,
X.Zhang,
G.J.Belsham,
and
S.Curry
(2010).
Foot-and-mouth disease virus 2C is a hexameric AAA+ protein with a coordinated ATP hydrolysis mechanism.
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J Biol Chem,
285,
24347-24359.
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A.W.Serohijos,
D.Tsygankov,
S.Liu,
T.C.Elston,
and
N.V.Dokholyan
(2009).
Multiscale approaches for studying energy transduction in dynein.
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Phys Chem Chem Phys,
11,
4840-4850.
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B.Chen,
T.A.Sysoeva,
S.Chowdhury,
L.Guo,
and
B.T.Nixon
(2009).
ADPase activity of recombinantly expressed thermotolerant ATPases may be caused by copurification of adenylate kinase of Escherichia coli.
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FEBS J,
276,
807-815.
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D.A.Kyriakidis,
and
E.Tiligada
(2009).
Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm.
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Amino Acids,
37,
443-458.
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J.D.Batchelor,
H.J.Sterling,
E.Hong,
E.R.Williams,
and
D.E.Wemmer
(2009).
Receiver domains control the active-state stoichiometry of Aquifex aeolicus sigma54 activator NtrC4, as revealed by electrospray ionization mass spectrometry.
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J Mol Biol,
393,
634-643.
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J.Peña-Sánchez,
S.Poggio,
U.Flores-Pérez,
A.Osorio,
C.Domenzain,
G.Dreyfus,
and
L.Camarena
(2009).
Identification of the binding site of the {sigma}54 hetero-oligomeric FleQ/FleT activator in the flagellar promoters of Rhodobacter sphaeroides.
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Microbiology,
155,
1669-1679.
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N.De,
M.V.Navarro,
R.V.Raghavan,
and
H.Sondermann
(2009).
Determinants for the activation and autoinhibition of the diguanylate cyclase response regulator WspR.
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J Mol Biol,
393,
619-633.
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PDB codes:
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N.Zhang,
N.Joly,
P.C.Burrows,
M.Jovanovic,
S.R.Wigneshweraraj,
and
M.Buck
(2009).
The role of the conserved phenylalanine in the sigma54-interacting GAFTGA motif of bacterial enhancer binding proteins.
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Nucleic Acids Res,
37,
5981-5992.
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P.C.Burrows,
J.Schumacher,
S.Amartey,
T.Ghosh,
T.A.Burgis,
X.Zhang,
B.T.Nixon,
and
M.Buck
(2009).
Functional roles of the pre-sensor I insertion sequence in an AAA+ bacterial enhancer binding protein.
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Mol Microbiol,
73,
519-533.
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P.C.Burrows,
N.Joly,
B.T.Nixon,
and
M.Buck
(2009).
Comparative analysis of activator-Esigma54 complexes formed with nucleotide-metal fluoride analogues.
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Nucleic Acids Res,
37,
5138-5150.
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P.C.Burrows,
N.Joly,
W.V.Cannon,
B.P.Cámara,
M.Rappas,
X.Zhang,
K.Dawes,
B.T.Nixon,
S.R.Wigneshweraraj,
and
M.Buck
(2009).
Coupling sigma factor conformation to RNA polymerase reorganisation for DNA melting.
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J Mol Biol,
387,
306-319.
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Q.Xu,
D.McMullan,
P.Abdubek,
T.Astakhova,
D.Carlton,
C.Chen,
H.J.Chiu,
T.Clayton,
D.Das,
M.C.Deller,
L.Duan,
M.A.Elsliger,
J.Feuerhelm,
J.Hale,
G.W.Han,
L.Jaroszewski,
K.K.Jin,
H.A.Johnson,
H.E.Klock,
M.W.Knuth,
P.Kozbial,
S.Sri Krishna,
A.Kumar,
D.Marciano,
M.D.Miller,
A.T.Morse,
E.Nigoghossian,
A.Nopakun,
L.Okach,
S.Oommachen,
J.Paulsen,
C.Puckett,
R.Reyes,
C.L.Rife,
N.Sefcovic,
C.Trame,
H.van den Bedem,
D.Weekes,
K.O.Hodgson,
J.Wooley,
A.M.Deacon,
A.Godzik,
S.A.Lesley,
and
I.A.Wilson
(2009).
A structural basis for the regulatory inactivation of DnaA.
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J Mol Biol,
385,
368-380.
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PDB code:
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T.R.Mack,
R.Gao,
and
A.M.Stock
(2009).
Probing the roles of the two different dimers mediated by the receiver domain of the response regulator PhoB.
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J Mol Biol,
389,
349-364.
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B.Chen,
T.A.Sysoeva,
S.Chowdhury,
and
B.T.Nixon
(2008).
Regulation and action of the bacterial enhancer-binding protein AAA+ domains.
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Biochem Soc Trans,
36,
89-93.
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G.Wisedchaisri,
M.Wu,
D.R.Sherman,
and
W.G.Hol
(2008).
Crystal structures of the response regulator DosR from Mycobacterium tuberculosis suggest a helix rearrangement mechanism for phosphorylation activation.
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J Mol Biol,
378,
227-242.
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PDB codes:
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J.M.Davies,
A.T.Brunger,
and
W.I.Weis
(2008).
Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change.
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Structure,
16,
715-726.
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PDB codes:
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M.D.Gonciarz,
F.G.Whitby,
D.M.Eckert,
C.Kieffer,
A.Heroux,
W.I.Sundquist,
and
C.P.Hill
(2008).
Biochemical and structural studies of yeast Vps4 oligomerization.
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J Mol Biol,
384,
878-895.
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PDB codes:
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M.Proell,
S.J.Riedl,
J.H.Fritz,
A.M.Rojas,
and
R.Schwarzenbacher
(2008).
The Nod-like receptor (NLR) family: a tale of similarities and differences.
|
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PLoS ONE,
3,
e2119.
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N.D.Thomsen,
and
J.M.Berger
(2008).
Structural frameworks for considering microbial protein- and nucleic acid-dependent motor ATPases.
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Mol Microbiol,
69,
1071-1090.
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N.Joly,
M.Rappas,
M.Buck,
and
X.Zhang
(2008).
Trapping of a transcription complex using a new nucleotide analogue: AMP aluminium fluoride.
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J Mol Biol,
375,
1206-1211.
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PDB code:
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R.Schnell,
D.Agren,
and
G.Schneider
(2008).
1.9 A structure of the signal receiver domain of the putative response regulator NarL from Mycobacterium tuberculosis.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
64,
1096-1100.
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PDB code:
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S.N.Joslin,
and
D.R.Hendrixson
(2008).
Analysis of the Campylobacter jejuni FlgR response regulator suggests integration of diverse mechanisms to activate an NtrC-like protein.
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J Bacteriol,
190,
2422-2433.
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T.Koyanagi,
T.Katayama,
H.Suzuki,
and
H.Kumagai
(2008).
Altered oligomerization properties of N316 mutants of Escherichia coli TyrR.
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J Bacteriol,
190,
8238-8243.
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X.Zhang,
and
D.B.Wigley
(2008).
The 'glutamate switch' provides a link between ATPase activity and ligand binding in AAA+ proteins.
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Nat Struct Mol Biol,
15,
1223-1227.
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A.Del Sol,
and
P.Carbonell
(2007).
The Modular Organization of Domain Structures: Insights into Protein-Protein Binding.
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PLoS Comput Biol,
3,
e239.
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A.J.Ninfa,
S.Selinsky,
N.Perry,
S.Atkins,
Q.Xiu Song,
A.Mayo,
D.Arps,
P.Woolf,
and
M.R.Atkinson
(2007).
Using two-component systems and other bacterial regulatory factors for the fabrication of synthetic genetic devices.
|
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Methods Enzymol,
422,
488-512.
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|
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B.Chen,
M.Doucleff,
D.E.Wemmer,
S.De Carlo,
H.H.Huang,
E.Nogales,
T.R.Hoover,
E.Kondrashkina,
L.Guo,
and
B.T.Nixon
(2007).
ATP ground- and transition states of bacterial enhancer binding AAA+ ATPases support complex formation with their target protein, sigma54.
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Structure,
15,
429-440.
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J.Kuriyan,
and
D.Eisenberg
(2007).
The origin of protein interactions and allostery in colocalization.
|
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Nature,
450,
983-990.
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L.L.Beck,
T.G.Smith,
and
T.R.Hoover
(2007).
Look, no hands! Unconventional transcriptional activators in bacteria.
|
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Trends Microbiol,
15,
530-537.
|
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M.N.Burtnick,
J.S.Downey,
P.J.Brett,
J.A.Boylan,
J.G.Frye,
T.R.Hoover,
and
F.C.Gherardini
(2007).
Insights into the complex regulation of rpoS in Borrelia burgdorferi.
|
| |
Mol Microbiol,
65,
277-293.
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M.Rappas,
D.Bose,
and
X.Zhang
(2007).
Bacterial enhancer-binding proteins: unlocking sigma54-dependent gene transcription.
|
| |
Curr Opin Struct Biol,
17,
110-116.
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R.Gao,
T.R.Mack,
and
A.M.Stock
(2007).
Bacterial response regulators: versatile regulatory strategies from common domains.
|
| |
Trends Biochem Sci,
32,
225-234.
|
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A.Costa,
T.Pape,
M.van Heel,
P.Brick,
A.Patwardhan,
and
S.Onesti
(2006).
Structural basis of the Methanothermobacter thermautotrophicus MCM helicase activity.
|
| |
Nucleic Acids Res,
34,
5829-5838.
|
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A.W.Serohijos,
Y.Chen,
F.Ding,
T.C.Elston,
and
N.V.Dokholyan
(2006).
A structural model reveals energy transduction in dynein.
|
| |
Proc Natl Acad Sci U S A,
103,
18540-18545.
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PDB code:
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J.P.Erzberger,
and
J.M.Berger
(2006).
Evolutionary relationships and structural mechanisms of AAA+ proteins.
|
| |
Annu Rev Biophys Biomol Struct,
35,
93.
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J.P.Erzberger,
M.L.Mott,
and
J.M.Berger
(2006).
Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling.
|
| |
Nat Struct Mol Biol,
13,
676-683.
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PDB code:
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M.A.Rubtsov,
Y.S.Polikanov,
V.A.Bondarenko,
Y.H.Wang,
and
V.M.Studitsky
(2006).
Chromatin structure can strongly facilitate enhancer action over a distance.
|
| |
Proc Natl Acad Sci U S A,
103,
17690-17695.
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M.G.Clarey,
J.P.Erzberger,
P.Grob,
A.E.Leschziner,
J.M.Berger,
E.Nogales,
and
M.Botchan
(2006).
Nucleotide-dependent conformational changes in the DnaA-like core of the origin recognition complex.
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Nat Struct Mol Biol,
13,
684-690.
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M.Rappas,
J.Schumacher,
H.Niwa,
M.Buck,
and
X.Zhang
(2006).
Structural basis of the nucleotide driven conformational changes in the AAA+ domain of transcription activator PspF.
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| |
J Mol Biol,
357,
481-492.
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PDB codes:
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M.Y.Galperin
(2006).
Structural classification of bacterial response regulators: diversity of output domains and domain combinations.
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| |
J Bacteriol,
188,
4169-4182.
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S.De Carlo,
B.Chen,
T.R.Hoover,
E.Kondrashkina,
E.Nogales,
and
B.T.Nixon
(2006).
The structural basis for regulated assembly and function of the transcriptional activator NtrC.
|
| |
Genes Dev,
20,
1485-1495.
|
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A.F.Neuwald
(2005).
Evolutionary clues to eukaryotic DNA clamp-loading mechanisms: analysis of the functional constraints imposed on replication factor C AAA+ ATPases.
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PDB codes:
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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
code is
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