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PDBsum entry 1caa
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Electron transport
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PDB id
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1caa
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Contents |
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* Residue conservation analysis
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DOI no:
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Protein Sci
1:1494-1507
(1992)
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PubMed id:
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X-ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus.
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M.W.Day,
B.T.Hsu,
L.Joshua-Tor,
J.B.Park,
Z.H.Zhou,
M.W.Adams,
D.C.Rees.
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ABSTRACT
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The structures of the oxidized and reduced forms of the rubredoxin from the
archaebacterium, Pyrococcus furiosus, an organism that grows optimally at 100
degrees C, have been determined by X-ray crystallography to a resolution of 1.8
A. Crystals of this rubredoxin grow in space group P2(1)2(1)2(1) with room
temperature cell dimensions a = 34.6 A, b = 35.5 A, and c = 44.4 A. Initial
phases were determined by the method of molecular replacement using the oxidized
form of the rubredoxin from the mesophilic eubacterium, Clostridium
pasteurianum, as a starting model. The oxidized and reduced models of P.
furiosus rubredoxin each contain 414 nonhydrogen protein atoms comprising 53
residues. The model of the oxidized form contains 61 solvent H2O oxygen atoms
and has been refined with X-PLOR and TNT to a final R = 0.178 with root mean
square (rms) deviations from ideality in bond distances and bond angles of 0.014
A and 2.06 degrees, respectively. The model of the reduced form contains 37
solvent H2O oxygen atoms and has been refined to R = 0.193 with rms deviations
from ideality in bond lengths of 0.012 A and in bond angles of 1.95 degrees. The
overall structure of P. furiosus rubredoxin is similar to the structures of
mesophilic rubredoxins, with the exception of a more extensive hydrogen-bonding
network in the beta-sheet region and multiple electrostatic interactions (salt
bridge, hydrogen bonds) of the Glu 14 side chain with groups on three other
residues (the amino-terminal nitrogen of Ala 1; the indole nitrogen of Trp 3;
and the amide nitrogen group of Phe 29). The influence of these and other
features upon the thermostability of the P. furiosus protein is discussed.
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Selected figure(s)
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Figure 2.
Fig. 2. Averagemainchainandsidechaintem-
eraure factors for the oxidized form. The
ainchainis shown y the solid ineandthe
idechainis shown by thedashed line.
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Figure 10.
Fig. 10. Stereo view of the pseudo-twofold
around the iron-sulfur cluster.
axis
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The above figures are
reprinted
from an Open Access publication published by the Protein Society:
Protein Sci
(1992,
1,
1494-1507)
copyright 1992.
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Figures were
selected
by an automated process.
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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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G.Mathies,
H.Blok,
J.A.Disselhorst,
P.Gast,
H.van der Meer,
D.M.Miedema,
R.M.Almeida,
J.J.Moura,
W.R.Hagen,
and
E.J.Groenen
(2011).
Continuous-wave EPR at 275GHz: application to high-spin Fe(3+) systems.
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J Magn Reson,
210,
126-132.
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T.Iwasaki
(2010).
Iron-sulfur world in aerobic and hyperthermoacidophilic archaea Sulfolobus.
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Archaea,
2010,
0.
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I.J.Lin,
B.Xia,
D.S.King,
T.E.Machonkin,
W.M.Westler,
and
J.L.Markley
(2009).
Hyperfine-Shifted (13)C and (15)N NMR Signals from Clostridium pasteurianum Rubredoxin: Extensive Assignments and Quantum Chemical Verification.
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J Am Chem Soc,
131,
15555-15563.
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K.Berka,
P.Hobza,
and
J.Vondrásek
(2009).
Analysis of energy stabilization inside the hydrophobic core of rubredoxin.
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Chemphyschem,
10,
543-548.
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K.L.Weiss,
F.Meilleur,
M.P.Blakeley,
and
D.A.Myles
(2008).
Preliminary neutron crystallographic analysis of selectively CH3-protonated deuterated rubredoxin from Pyrococcus furiosus.
|
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
64,
537-540.
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M.Proudfoot,
S.A.Sanders,
A.Singer,
R.Zhang,
G.Brown,
A.Binkowski,
L.Xu,
J.A.Lukin,
A.G.Murzin,
A.Joachimiak,
C.H.Arrowsmith,
A.M.Edwards,
A.V.Savchenko,
and
A.F.Yakunin
(2008).
Biochemical and structural characterization of a novel family of cystathionine beta-synthase domain proteins fused to a Zn ribbon-like domain.
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J Mol Biol,
375,
301-315.
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PDB codes:
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B.J.Henriques,
L.M.Saraiva,
and
C.M.Gomes
(2006).
Combined spectroscopic and calorimetric characterisation of rubredoxin reversible thermal transition.
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J Biol Inorg Chem,
11,
73-81.
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M.L.Tan,
C.Kang,
and
T.Ichiye
(2006).
The role of backbone stability near Ala44 in the high reduction potential class of rubredoxins.
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Proteins,
62,
708-714.
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T.Iwasaki,
A.Kounosu,
D.Ohmori,
and
T.Kumasaka
(2006).
Crystallization and preliminary X-ray diffraction studies of a hyperthermophilic Rieske protein variant (SDX-triple) with an engineered rubredoxin-like mononuclear iron site.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
62,
993-995.
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A.M.Grunden,
F.E.Jenney,
K.Ma,
M.Ji,
M.V.Weinberg,
and
M.W.Adams
(2005).
In vitro reconstitution of an NADPH-dependent superoxide reduction pathway from Pyrococcus furiosus.
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Appl Environ Microbiol,
71,
1522-1530.
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D.M.LeMaster,
and
G.Hernández
(2005).
Additivity in both thermodynamic stability and thermal transition temperature for rubredoxin chimeras via hybrid native partitioning.
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Structure,
13,
1153-1163.
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D.M.LeMaster,
J.Tang,
D.I.Paredes,
and
G.Hernández
(2005).
Enhanced thermal stability achieved without increased conformational rigidity at physiological temperatures: spatial propagation of differential flexibility in rubredoxin hybrids.
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Proteins,
61,
608-616.
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H.Bönisch,
C.L.Schmidt,
P.Bianco,
and
R.Ladenstein
(2005).
Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 A X-ray structure of mutant W4L/R5S.
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Acta Crystallogr D Biol Crystallogr,
61,
990.
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PDB codes:
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D.M.LeMaster,
J.Tang,
and
G.Hernández
(2004).
Absence of kinetic thermal stabilization in a hyperthermophile rubredoxin indicated by 40 microsecond folding in the presence of irreversible denaturation.
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Proteins,
57,
118-127.
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D.Triantafillidou,
E.Persidou,
D.Lazarou,
P.Andrikopoulos,
F.Leontiadou,
and
T.Choli-Papadopoulou
(2004).
Structural destabilization of the recombinant thermophilic TthL11 ribosomal protein by a single amino acid substitution.
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Biol Chem,
385,
31-39.
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K.Kurihara,
I.Tanaka,
T.Chatake,
M.W.Adams,
F.E.Jenney,
N.Moiseeva,
R.Bau,
and
N.Niimura
(2004).
Neutron crystallographic study on rubredoxin from Pyrococcus furiosus by BIX-3, a single-crystal diffractometer for biomacromolecules.
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Proc Natl Acad Sci U S A,
101,
11215-11220.
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PDB code:
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M.A.Pysz,
S.B.Conners,
C.I.Montero,
K.R.Shockley,
M.R.Johnson,
D.E.Ward,
and
R.M.Kelly
(2004).
Transcriptional analysis of biofilm formation processes in the anaerobic, hyperthermophilic bacterium Thermotoga maritima.
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Appl Environ Microbiol,
70,
6098-6112.
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T.Chatake,
K.Kurihara,
I.Tanaka,
I.Tsyba,
R.Bau,
F.E.Jenney,
M.W.Adams,
and
N.Niimura
(2004).
A neutron crystallographic analysis of a rubredoxin mutant at 1.6 A resolution.
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Acta Crystallogr D Biol Crystallogr,
60,
1364-1373.
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PDB codes:
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Y.Hioki,
K.Ogasahara,
S.J.Lee,
J.Ma,
M.Ishida,
Y.Yamagata,
Y.Matsuura,
M.Ota,
M.Ikeguchi,
S.Kuramitsu,
and
K.Yutani
(2004).
The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus. Investigation of stabilization factors.
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Eur J Biochem,
271,
2624-2635.
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PDB code:
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A.Grottesi,
M.A.Ceruso,
A.Colosimo,
and
A.Di Nola
(2002).
Molecular dynamics study of a hyperthermophilic and a mesophilic rubredoxin.
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Proteins,
46,
287-294.
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B.Cobucci-Ponzano,
M.Moracci,
B.Di Lauro,
M.Ciaramella,
R.D'Avino,
and
M.Rossi
(2002).
Ionic network at the C-terminus of the beta-glycosidase from the hyperthermophilic archaeon Sulfolobus solfataricus: Functional role in the quaternary structure thermal stabilization.
|
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Proteins,
48,
98.
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T.A.Ramelot,
J.R.Cort,
A.A.Yee,
A.Semesi,
A.M.Edwards,
C.H.Arrowsmith,
and
M.A.Kennedy
(2002).
NMR structure of the Escherichia coli protein YacG: a novel sequence motif in the zinc-finger family of proteins.
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Proteins,
49,
289-293.
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PDB code:
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K.Numata,
Y.Hayashi-Iwasaki,
J.Kawaguchi,
M.Sakurai,
H.Moriyama,
N.Tanaka,
and
T.Oshima
(2001).
Thermostabilization of a chimeric enzyme by residue substitutions: four amino acid residues in loop regions are responsible for the thermostability of Thermus thermophilus isopropylmalate dehydrogenase.
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Biochim Biophys Acta,
1545,
174-183.
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T.Min,
C.E.Ergenekan,
M.K.Eidsness,
T.Ichiye,
and
C.Kang
(2001).
Leucine 41 is a gate for water entry in the reduction of Clostridium pasteurianum rubredoxin.
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Protein Sci,
10,
613-621.
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PDB codes:
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W.Schüler,
K.Kloiber,
T.Matt,
K.Bister,
and
R.Konrat
(2001).
Application of cross-correlated NMR spin relaxation to the zinc-finger protein CRP2(LIM2): evidence for collective motions in LIM domains.
|
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Biochemistry,
40,
9596-9604.
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PDB code:
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A.P.Yeh,
Y.Hu,
F.E.Jenney,
M.W.Adams,
and
D.C.Rees
(2000).
Structures of the superoxide reductase from Pyrococcus furiosus in the oxidized and reduced states.
|
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Biochemistry,
39,
2499-2508.
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PDB codes:
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F.Bonomi,
D.Fessas,
S.Iametti,
D.M.Kurtz,
and
S.Mazzini
(2000).
Thermal stability of Clostridium pasteurianum rubredoxin: deconvoluting the contributions of the metal site and the protein.
|
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Protein Sci,
9,
2413-2426.
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G.Hernandez,
F.E.Jenney,
M.W.Adams,
and
D.M.LeMaster
(2000).
Millisecond time scale conformational flexibility in a hyperthermophile protein at ambient temperature.
|
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Proc Natl Acad Sci U S A,
97,
3166-3170.
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K.Schweimer,
S.Hoffmann,
J.Wastl,
U.G.Maier,
P.Rösch,
and
H.Sticht
(2000).
Solution structure of a zinc substituted eukaryotic rubredoxin from the cryptomonad alga Guillardia theta.
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Protein Sci,
9,
1474-1486.
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PDB codes:
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P.Strop,
and
S.L.Mayo
(2000).
Contribution of surface salt bridges to protein stability.
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Biochemistry,
39,
1251-1255.
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PDB code:
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R.Jaenicke
(2000).
Do ultrastable proteins from hyperthermophiles have high or low conformational rigidity?
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Proc Natl Acad Sci U S A,
97,
2962-2964.
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S.Frillingos,
A.Linden,
F.Niehaus,
C.Vargas,
J.J.Nieto,
A.Ventosa,
G.Antranikian,
and
C.Drainas
(2000).
Cloning and expression of alpha-amylase from the hyperthermophilic archaeon Pyrococcus woesei in the moderately halophilic bacterium Halomonas elongata.
|
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J Appl Microbiol,
88,
495-503.
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C.G.Schipke,
D.B.Goodin,
D.E.McRee,
and
C.D.Stout
(1999).
Oxidized and reduced Azotobacter vinelandii ferredoxin I at 1.4 A resolution: conformational change of surface residues without significant change in the [3Fe-4S]+/0 cluster.
|
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Biochemistry,
38,
8228-8239.
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PDB codes:
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C.Li,
J.Heatwole,
S.Soelaiman,
and
M.Shoham
(1999).
Crystal structure of a thermophilic alcohol dehydrogenase substrate complex suggests determinants of substrate specificity and thermostability.
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Proteins,
37,
619-627.
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PDB code:
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L.D.Gillès de Pélichy,
and
E.T.Smith
(1999).
Redox properties of mesophilic and hyperthermophilic rubredoxins as a function of pressure and temperature.
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Biochemistry,
38,
7874-7880.
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M.J.Maher,
Z.Xiao,
M.C.Wilce,
J.M.Guss,
and
A.G.Wedd
(1999).
Rubredoxin from Clostridium pasteurianum. Structures of G10A, G43A and G10VG43A mutant proteins. Mutation of conserved glycine 10 to valine causes the 9-10 peptide link to invert.
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Acta Crystallogr D Biol Crystallogr,
55,
962-968.
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PDB codes:
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M.K.Eidsness,
A.E.Burden,
K.A.Richie,
D.M.Kurtz,
R.A.Scott,
E.T.Smith,
T.Ichiye,
B.Beard,
T.Min,
and
C.Kang
(1999).
Modulation of the redox potential of the [Fe(SCys)(4)] site in rubredoxin by the orientation of a peptide dipole.
|
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Biochemistry,
38,
14803-14809.
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PDB code:
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M.M.Sun,
N.Tolliday,
C.Vetriani,
F.T.Robb,
and
D.S.Clark
(1999).
Pressure-induced thermostabilization of glutamate dehydrogenase from the hyperthermophile Pyrococcus furiosus.
|
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Protein Sci,
8,
1056-1063.
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R.Morales,
M.H.Charon,
G.Hudry-Clergeon,
Y.Pétillot,
S.Norager,
M.Medina,
and
M.Frey
(1999).
Refined X-ray structures of the oxidized, at 1.3 A, and reduced, at 1.17 A, [2Fe-2S] ferredoxin from the cyanobacterium Anabaena PCC7119 show redox-linked conformational changes.
|
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Biochemistry,
38,
15764-15773.
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PDB codes:
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B.Wang,
D.N.Jones,
B.P.Kaine,
and
M.A.Weiss
(1998).
High-resolution structure of an archaeal zinc ribbon defines a general architectural motif in eukaryotic RNA polymerases.
|
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Structure,
6,
555-569.
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PDB code:
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E.Farinas,
and
L.Regan
(1998).
The de novo design of a rubredoxin-like Fe site.
|
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Protein Sci,
7,
1939-1946.
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K.C.Usher,
A.F.de la Cruz,
F.W.Dahlquist,
R.V.Swanson,
M.I.Simon,
and
S.J.Remington
(1998).
Crystal structures of CheY from Thermotoga maritima do not support conventional explanations for the structural basis of enhanced thermostability.
|
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Protein Sci,
7,
403-412.
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PDB codes:
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K.Ogasahara,
E.A.Lapshina,
M.Sakai,
Y.Izu,
S.Tsunasawa,
I.Kato,
and
K.Yutani
(1998).
Electrostatic stabilization in methionine aminopeptidase from hyperthermophile Pyrococcus furiosus.
|
| |
Biochemistry,
37,
5939-5946.
|
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K.Ogasahara,
M.Nakamura,
S.Nakura,
S.Tsunasawa,
I.Kato,
T.Yoshimoto,
and
K.Yutani
(1998).
The unusually slow unfolding rate causes the high stability of pyrrolidone carboxyl peptidase from a hyperthermophile, Pyrococcus furiosus: equilibrium and kinetic studies of guanidine hydrochloride-induced unfolding and refolding.
|
| |
Biochemistry,
37,
17537-17544.
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M.W.Adams,
and
R.M.Kelly
(1998).
Finding and using hyperthermophilic enzymes.
|
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Trends Biotechnol,
16,
329-332.
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M.W.Bauer,
and
R.M.Kelly
(1998).
The family 1 beta-glucosidases from Pyrococcus furiosus and Agrobacterium faecalis share a common catalytic mechanism.
|
| |
Biochemistry,
37,
17170-17178.
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S.Cavagnero,
D.A.Debe,
Z.H.Zhou,
M.W.Adams,
and
S.I.Chan
(1998).
Kinetic role of electrostatic interactions in the unfolding of hyperthermophilic and mesophilic rubredoxins.
|
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Biochemistry,
37,
3369-3376.
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S.Cavagnero,
Z.H.Zhou,
M.W.Adams,
and
S.I.Chan
(1998).
Unfolding mechanism of rubredoxin from Pyrococcus furiosus.
|
| |
Biochemistry,
37,
3377-3385.
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V.Villeret,
B.Clantin,
C.Tricot,
C.Legrain,
M.Roovers,
V.Stalon,
N.Glansdorff,
and
J.Van Beeumen
(1998).
The crystal structure of Pyrococcus furiosus ornithine carbamoyltransferase reveals a key role for oligomerization in enzyme stability at extremely high temperatures.
|
| |
Proc Natl Acad Sci U S A,
95,
2801-2806.
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PDB code:
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G.Auerbach,
R.Huber,
M.Grättinger,
K.Zaiss,
H.Schurig,
R.Jaenicke,
and
U.Jacob
(1997).
Closed structure of phosphoglycerate kinase from Thermotoga maritima reveals the catalytic mechanism and determinants of thermal stability.
|
| |
Structure,
5,
1475-1483.
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PDB code:
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J.R.Kiefer,
C.Mao,
C.J.Hansen,
S.L.Basehore,
H.H.Hogrefe,
J.C.Braman,
and
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Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution.
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L.Prade,
P.Hof,
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Dimer interface of glutathione S-transferase from Arabidopsis thaliana: influence of the G-site architecture on the dimer interface and implications for classification.
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Biochemistry,
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PDB code:
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M.K.Eidsness,
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The crystal structure of citrate synthase from the hyperthermophilic archaeon pyrococcus furiosus at 1.9 A resolution,.
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Biochemistry,
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PDB code:
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D.W.Rice,
K.S.Yip,
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Determinants of enzyme thermostability observed in the molecular structure of Thermus aquaticus D-glyceraldehyde-3-phosphate dehydrogenase at 25 Angstroms Resolution.
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Biochemistry,
35,
2597-2609.
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PDB code:
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K.A.Richie,
Q.Teng,
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Protein Sci,
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Molecular model of the solution structure for the paramagnetic four-iron ferredoxin from the hyperthermophilic archaeon Thermococcus litoralis.
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Biochemistry,
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Structure,
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PDB code:
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Z.Dauter,
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Zinc- and iron-rubredoxins from Clostridium pasteurianum at atomic resolution: a high-precision model of a ZnS4 coordination unit in a protein.
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Proc Natl Acad Sci U S A,
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PDB codes:
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A.Goldman
(1995).
How to make my blood boil.
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Structure,
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1277-1279.
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Structure,
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The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures.
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Structure,
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PDB codes:
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M.Hennig,
B.Darimont,
R.Sterner,
K.Kirschner,
and
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2.0 A structure of indole-3-glycerol phosphate synthase from the hyperthermophile Sulfolobus solfataricus: possible determinants of protein stability.
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| |
Structure,
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PDB code:
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M.W.Adams,
F.B.Perler,
and
R.M.Kelly
(1995).
Extremozymes: expanding the limits of biocatalysis.
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Molecular dynamics simulations of rubredoxin from Clostridium pasteurianum: changes in structure and electrostatic potential during redox reactions.
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Proteins,
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Synthesis and characterization of Desulfovibrio gigas rubredoxin and rubredoxin fragments.
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M.W.Adams
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Protein Sci,
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(1993).
Structures of DNA-binding mutant zinc finger domains: implications for DNA binding.
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Protein Sci,
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PDB codes:
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V.S.Shenoy,
and
T.Ichiye
(1993).
Influence of protein flexibility on the redox potential of rubredoxin: energy minimization studies.
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Proteins,
17,
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P.R.Blake,
J.B.Park,
Z.H.Zhou,
D.R.Hare,
M.W.Adams,
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Solution-state structure by NMR of zinc-substituted rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus.
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Protein Sci,
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1508-1521.
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PDB code:
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|
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|
|
P.R.Blake,
M.W.Day,
B.T.Hsu,
L.Joshua-Tor,
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M.W.Adams,
D.C.Rees,
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(1992).
Comparison of the X-ray structure of native rubredoxin from Pyrococcus furiosus with the NMR structure of the zinc-substituted protein.
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Protein Sci,
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1522-1525.
|
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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
codes are
shown on the right.
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|
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