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PDBsum entry 1doi
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Electron transport
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PDB id
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1doi
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Contents |
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* Residue conservation analysis
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Nat Struct Biol
3:452-458
(1996)
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PubMed id:
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Insights into protein adaptation to a saturated salt environment from the crystal structure of a halophilic 2Fe-2S ferredoxin.
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F.Frolow,
M.Harel,
J.L.Sussman,
M.Mevarech,
M.Shoham.
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ABSTRACT
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Haloarcula marismortui is an archaebacterium that flourishes in the world's
saltiest body of water, the Dead Sea. The cytosol of this organism is a
supersaturated salt solution in which proteins are soluble and active. The
crystal structure of a 2Fe-2S ferredoxin from H. marismortui determined at 1.9 A
is similar to those of plant-type 2Fe-2S ferredoxins of known structure, with
two important distinctions. The entire surface of the protein is coated with
acidic residues except for the vicinity of the iron-sulphur cluster, and there
is an insertion of two amphipathic helices near the N-terminus. These form a
separate hyperacidic domain whose postulated function to provide extra surface
carboxylates for solvation. These data and the fact that bound surface water
molecules have on the average 40% more hydrogen bonds than in a typical
non-halophilic protein crystal structure support the notion that haloadaptation
involves better water binding capacity.
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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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R.Nechushtai,
H.Lammert,
D.Michaeli,
Y.Eisenberg-Domovich,
J.A.Zuris,
M.A.Luca,
D.T.Capraro,
A.Fish,
O.Shimshon,
M.Roy,
A.Schug,
P.C.Whitford,
O.Livnah,
J.N.Onuchic,
and
P.A.Jennings
(2011).
Allostery in the ferredoxin protein motif does not involve a conformational switch.
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Proc Natl Acad Sci U S A,
108,
2240-2245.
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PDB code:
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K.Wada,
M.Irie,
H.Suzuki,
and
K.Fukuyama
(2010).
Crystal structure of the halotolerant gamma-glutamyltranspeptidase from Bacillus subtilis in complex with glutamate reveals a unique architecture of the solvent-exposed catalytic pocket.
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FEBS J,
277,
1000-1009.
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PDB code:
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M.Toth,
C.Smith,
H.Frase,
S.Mobashery,
and
S.Vakulenko
(2010).
An antibiotic-resistance enzyme from a deep-sea bacterium.
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J Am Chem Soc,
132,
816-823.
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PDB code:
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J.A.Winter,
P.Christofi,
S.Morroll,
and
K.A.Bunting
(2009).
The crystal structure of Haloferax volcanii proliferating cell nuclear antigen reveals unique surface charge characteristics due to halophilic adaptation.
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BMC Struct Biol,
9,
55.
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PDB code:
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H.Tokunaga,
T.Arakawa,
and
M.Tokunaga
(2008).
Engineering of halophilic enzymes: two acidic amino acid residues at the carboxy-terminal region confer halophilic characteristics to Halomonas and Pseudomonas nucleoside diphosphate kinases.
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Protein Sci,
17,
1603-1610.
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J.Meyer
(2008).
Iron-sulfur protein folds, iron-sulfur chemistry, and evolution.
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J Biol Inorg Chem,
13,
157-170.
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J.Pandhal,
A.P.Snijders,
P.C.Wright,
and
C.A.Biggs
(2008).
A cross-species quantitative proteomic study of salt adaptation in a halotolerant environmental isolate using 15N metabolic labelling.
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Proteomics,
8,
2266-2284.
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S.Paul,
S.K.Bag,
S.Das,
E.T.Harvill,
and
C.Dutta
(2008).
Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes.
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Genome Biol,
9,
R70.
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Y.Cao,
L.Liao,
X.W.Xu,
A.Oren,
C.Wang,
X.F.Zhu,
and
M.Wu
(2008).
Characterization of alcohol dehydrogenase from the haloalkaliphilic archaeon Natronomonas pharaonis.
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Extremophiles,
12,
471-476.
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A.K.Bandyopadhyay,
G.Krishnamoorthy,
L.C.Padhy,
and
H.M.Sonawat
(2007).
Kinetics of salt-dependent unfolding of [2Fe-2S] ferredoxin of Halobacterium salinarum.
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Extremophiles,
11,
615-625.
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K.Yoshimatsu,
O.Araya,
and
T.Fujiwara
(2007).
Haloarcula marismortui cytochrome b-561 is encoded by the narC gene in the dissimilatory nitrate reductase operon.
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Extremophiles,
11,
41-47.
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M.Tehei,
B.Franzetti,
K.Wood,
F.Gabel,
E.Fabiani,
M.Jasnin,
M.Zamponi,
D.Oesterhelt,
G.Zaccai,
M.Ginzburg,
and
B.Z.Ginzburg
(2007).
Neutron scattering reveals extremely slow cell water in a Dead Sea organism.
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Proc Natl Acad Sci U S A,
104,
766-771.
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S.R.Trevino,
J.M.Scholtz,
and
C.N.Pace
(2007).
Amino acid contribution to protein solubility: Asp, Glu, and Ser contribute more favorably than the other hydrophilic amino acids in RNase Sa.
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J Mol Biol,
366,
449-460.
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T.Fujii,
T.Oikawa,
I.Muraoka,
K.Soda,
and
Y.Hata
(2007).
Crystallization and preliminary X-ray diffraction studies of tetrameric malate dehydrogenase from the novel Antarctic psychrophile Flavobacterium frigidimaris KUC-1.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
63,
983-986.
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Y.Sato,
and
M.Nishida
(2007).
Post-duplication charge evolution of phosphoglucose isomerases in teleost fishes through weak selection on many amino acid sites.
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BMC Evol Biol,
7,
204.
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K.L.Britton,
P.J.Baker,
M.Fisher,
S.Ruzheinikov,
D.J.Gilmour,
M.J.Bonete,
J.Ferrer,
C.Pire,
J.Esclapez,
and
D.W.Rice
(2006).
Analysis of protein solvent interactions in glucose dehydrogenase from the extreme halophile Haloferax mediterranei.
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Proc Natl Acad Sci U S A,
103,
4846-4851.
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PDB codes:
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K.Manikandan,
A.Bhardwaj,
N.Gupta,
N.K.Lokanath,
A.Ghosh,
V.S.Reddy,
and
S.Ramakumar
(2006).
Crystal structures of native and xylosaccharide-bound alkali thermostable xylanase from an alkalophilic Bacillus sp. NG-27: structural insights into alkalophilicity and implications for adaptation to polyextreme conditions.
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Protein Sci,
15,
1951-1960.
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PDB codes:
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J.Esclapez,
K.L.Britton,
P.J.Baker,
M.Fisher,
C.Pire,
J.Ferrer,
M.J.Bonete,
and
D.W.Rice
(2005).
Crystallization and preliminary X-ray analysis of binary and ternary complexes of Haloferax mediterranei glucose dehydrogenase.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
61,
743-746.
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K.Ozawa,
T.Harashina,
R.Yatsunami,
and
S.Nakamura
(2005).
Gene cloning, expression and partial characterization of cell division protein FtsZ1 from extremely halophilic archaeon Haloarcula japonica strain TR-1.
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Extremophiles,
9,
281-288.
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L.Premkumar,
H.M.Greenblatt,
U.K.Bageshwar,
T.Savchenko,
I.Gokhman,
J.L.Sussman,
and
A.Zamir
(2005).
Three-dimensional structure of a halotolerant algal carbonic anhydrase predicts halotolerance of a mammalian homolog.
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Proc Natl Acad Sci U S A,
102,
7493-7498.
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PDB code:
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A.Barzilai,
S.Kumar,
H.Wolfson,
and
R.Nussinov
(2004).
Potential folding-function interrelationship in proteins.
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Proteins,
56,
635-649.
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D.Madern,
M.Camacho,
A.Rodríguez-Arnedo,
M.J.Bonete,
and
G.Zaccai
(2004).
Salt-dependent studies of NADP-dependent isocitrate dehydrogenase from the halophilic archaeon Haloferax volcanii.
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Extremophiles,
8,
377-384.
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B.Franzetti,
G.Schoehn,
D.Garcia,
R.W.Ruigrok,
and
G.Zaccai
(2002).
Characterization of the proteasome from the extremely halophilic archaeon Haloarcula marismortui.
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Archaea,
1,
53-61.
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B.Mamat,
A.Roth,
C.Grimm,
U.Ermler,
C.Tziatzios,
D.Schubert,
R.K.Thauer,
and
S.Shima
(2002).
Crystal structures and enzymatic properties of three formyltransferases from archaea: environmental adaptation and evolutionary relationship.
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Protein Sci,
11,
2168-2178.
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PDB codes:
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I.Bertini,
C.Luchinat,
A.Provenzani,
A.Rosato,
and
P.R.Vasos
(2002).
Browsing gene banks for Fe2S2 ferredoxins and structural modeling of 88 plant-type sequences: an analysis of fold and function.
|
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Proteins,
46,
110-127.
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J.Meyer,
M.D.Clay,
M.K.Johnson,
A.Stubna,
E.Münck,
C.Higgins,
and
P.Wittung-Stafshede
(2002).
A hyperthermophilic plant-type [2Fe-2S] ferredoxin from Aquifex aeolicus is stabilized by a disulfide bond.
|
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Biochemistry,
41,
3096-3108.
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A.K.Bandyopadhyay,
G.Krishnamoorthy,
and
H.M.Sonawat
(2001).
Structural stabilization of [2Fe-2S] ferredoxin from Halobacterium salinarum.
|
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Biochemistry,
40,
1284-1292.
|
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H.Ichiki,
Y.Tanaka,
K.Mochizuki,
K.Yoshimatsu,
T.Sakurai,
and
T.Fujiwara
(2001).
Purification, characterization, and genetic analysis of Cu-containing dissimilatory nitrite reductase from a denitrifying halophilic archaeon, Haloarcula marismortui.
|
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J Bacteriol,
183,
4149-4156.
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A.K.Bandyopadhyay,
and
H.M.Sonawat
(2000).
Salt dependent stability and unfolding of [Fe2-S2] ferredoxin of Halobacterium salinarum: spectroscopic investigations.
|
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Biophys J,
79,
501-510.
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M.C.Wahl,
G.P.Bourenkov,
H.D.Bartunik,
and
R.Huber
(2000).
Flexibility, conformational diversity and two dimerization modes in complexes of ribosomal protein L12.
|
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EMBO J,
19,
174-186.
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PDB codes:
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M.Mevarech,
F.Frolow,
and
L.M.Gloss
(2000).
Halophilic enzymes: proteins with a grain of salt.
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Biophys Chem,
86,
155-164.
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S.B.Richard,
D.Madern,
E.Garcin,
and
G.Zaccai
(2000).
Halophilic adaptation: novel solvent protein interactions observed in the 2.9 and 2.6 A resolution structures of the wild type and a mutant of malate dehydrogenase from Haloarcula marismortui.
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Biochemistry,
39,
992.
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PDB codes:
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C.Ebel,
P.Faou,
B.Kernel,
and
G.Zaccai
(1999).
Relative role of anions and cations in the stabilization of halophilic malate dehydrogenase.
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Biochemistry,
38,
9039-9047.
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C.Wanner,
and
J.Soppa
(1999).
Genetic identification of three ABC transporters as essential elements for nitrate respiration in Haloferax volcanii.
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Genetics,
152,
1417-1428.
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D.W.Hough,
and
M.J.Danson
(1999).
Extremozymes.
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Curr Opin Chem Biol,
3,
39-46.
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H.L.Wilson,
H.C.Aldrich,
and
J.Maupin-Furlow
(1999).
Halophilic 20S proteasomes of the archaeon Haloferax volcanii: purification, characterization, and gene sequence analysis.
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J Bacteriol,
181,
5814-5824.
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K.Kojoh,
H.Matsuzawa,
and
T.Wakagi
(1999).
Zinc and an N-terminal extra stretch of the ferredoxin from a thermoacidophilic archaeon stabilize the molecule at high temperature.
|
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Eur J Biochem,
264,
85-91.
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M.T.Bes,
E.Parisini,
L.A.Inda,
L.M.Saraiva,
M.L.Peleato,
and
G.M.Sheldrick
(1999).
Crystal structure determination at 1.4 A resolution of ferredoxin from the green alga Chlorella fusca.
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Structure,
7,
1201-1211.
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PDB code:
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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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S.Y.Kim,
K.Y.Hwang,
S.H.Kim,
H.C.Sung,
Y.S.Han,
and
Y.Cho
(1999).
Structural basis for cold adaptation. Sequence, biochemical properties, and crystal structure of malate dehydrogenase from a psychrophile Aquaspirillium arcticum.
|
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J Biol Chem,
274,
11761-11767.
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PDB codes:
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W.Grabarse,
M.Vaupel,
J.A.Vorholt,
S.Shima,
R.K.Thauer,
A.Wittershagen,
G.Bourenkov,
H.D.Bartunik,
and
U.Ermler
(1999).
The crystal structure of methenyltetrahydromethanopterin cyclohydrolase from the hyperthermophilic archaeon Methanopyrus kandleri.
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Structure,
7,
1257-1268.
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PDB code:
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A.Müller,
J.J.Müller,
Y.A.Muller,
H.Uhlmann,
R.Bernhardt,
and
U.Heinemann
(1998).
New aspects of electron transfer revealed by the crystal structure of a truncated bovine adrenodoxin, Adx(4-108).
|
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Structure,
6,
269-280.
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PDB code:
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K.L.Britton,
T.J.Stillman,
K.S.Yip,
P.Forterre,
P.C.Engel,
and
D.W.Rice
(1998).
Insights into the molecular basis of salt tolerance from the study of glutamate dehydrogenase from Halobacterium salinarum.
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J Biol Chem,
273,
9023-9030.
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M.J.Danson,
and
D.W.Hough
(1998).
Structure, function and stability of enzymes from the Archaea.
|
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Trends Microbiol,
6,
307-314.
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R.Jaenicke,
and
G.Böhm
(1998).
The stability of proteins in extreme environments.
|
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Curr Opin Struct Biol,
8,
738-748.
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U.Pieper,
G.Kapadia,
M.Mevarech,
and
O.Herzberg
(1998).
Structural features of halophilicity derived from the crystal structure of dihydrofolate reductase from the Dead Sea halophilic archaeon, Haloferax volcanii.
|
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Structure,
6,
75-88.
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PDB code:
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J.Soppa,
and
T.A.Link
(1997).
The TATA-box-binding protein (TBP) of Halobacterium salinarum. Cloning of the tbp gene, heterologous production of TBP and folding of TBP into a native conformation.
|
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Eur J Biochem,
249,
318-324.
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P.P.Dennis,
and
L.C.Shimmin
(1997).
Evolutionary divergence and salinity-mediated selection in halophilic archaea.
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Microbiol Mol Biol Rev,
61,
90.
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T.Fujii,
Y.Hata,
M.Oozeki,
H.Moriyama,
T.Wakagi,
N.Tanaka,
and
T.Oshima
(1997).
The crystal structure of zinc-containing ferredoxin from the thermoacidophilic archaeon Sulfolobus sp. strain 7.
|
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Biochemistry,
36,
1505-1513.
|
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U.Ermler,
M.Merckel,
R.Thauer,
and
S.Shima
(1997).
Formylmethanofuran: tetrahydromethanopterin formyltransferase from Methanopyrus kandleri - new insights into salt-dependence and thermostability.
|
| |
Structure,
5,
635-646.
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PDB code:
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W.P.Burmeister,
S.Cottaz,
H.Driguez,
R.Iori,
S.Palmieri,
and
B.Henrissat
(1997).
The crystal structures of Sinapis alba myrosinase and a covalent glycosyl-enzyme intermediate provide insights into the substrate recognition and active-site machinery of an S-glycosidase.
|
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Structure,
5,
663-675.
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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
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.
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Links
