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* Residue conservation analysis
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Enzyme class:
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E.C.3.2.1.1
- Alpha-amylase.
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Reaction:
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Endohydrolysis of 1,4-alpha-glucosidic linkages in oligosaccharides and polysaccharides.
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Gene Ontology (GO) functional annotation
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Biological process
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carbohydrate metabolic process
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1 term
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Biochemical function
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catalytic activity
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2 terms
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DOI no:
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Structure
6:1503-1516
(1998)
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PubMed id:
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Structures of the psychrophilic Alteromonas haloplanctis alpha-amylase give insights into cold adaptation at a molecular level.
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N.Aghajari,
G.Feller,
C.Gerday,
R.Haser.
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ABSTRACT
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Background:. Enzymes from psychrophilic (cold-adapted) microorganisms operate at
temperatures close to 0 degreesC, where the activity of their mesophilic and
thermophilic counterparts is drastically reduced. It has generally been assumed
that thermophily is associated with rigid proteins, whereas psychrophilic
enzymes have a tendency to be more flexible. Results:. Insights into the cold
adaptation of proteins are gained on the basis of a psychrophilic protein's
molecular structure. To this end, we have determined the structure of the
recombinant form of a psychrophilic alpha-amylase from Alteromonas haloplanctis
at 2.4 A resolution. We have compared this with the structure of the wild-type
enzyme, recently solved at 2.0 A resolution, and with available structures of
their mesophilic counterparts. These comparative studies have enabled us to
identify possible determinants of cold adaptation. Conclusions:. We propose that
an increased resilience of the molecular surface and a less rigid protein core,
with less interdomain interactions, are determining factors of the
conformational flexibility that allows efficient enzyme catalysis in cold
environments.
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Selected figure(s)
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Figure 4.
Figure 4. A representation of charges at the surfaces of
(a) AHA, (b) HPA and (c) BLA, displayed at the same potential
range. Color codes are: red, aspartic and glutamic acids; blue,
lysines and arginines. This figure was generated with the
program GRASP [57].
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1998,
6,
1503-1516)
copyright 1998.
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Figure was
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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S.Ben Mabrouk,
N.Aghajari,
M.Ben Ali,
E.Ben Messaoud,
M.Juy,
R.Haser,
and
S.Bejar
(2011).
Enhancement of the thermostability of the maltogenic amylase MAUS149 by Gly312Ala and Lys436Arg substitutions.
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Bioresour Technol, 102,
1740-1746.
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E.Champion,
M.Remaud-Simeon,
L.K.Skov,
J.S.Kastrup,
M.Gajhede,
and
O.Mirza
(2009).
The apo structure of sucrose hydrolase from Xanthomonas campestris pv. campestris shows an open active-site groove.
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Acta Crystallogr D Biol Crystallogr, 65,
1309-1314.
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H.L.Pedersen,
N.P.Willassen,
and
I.Leiros
(2009).
The first structure of a cold-adapted superoxide dismutase (SOD): biochemical and structural characterization of iron SOD from Aliivibrio salmonicida.
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Acta Crystallogr Sect F Struct Biol Cryst Commun, 65,
84-92.
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PDB code:
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T.P.Schrank,
D.W.Bolen,
and
V.J.Hilser
(2009).
Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins.
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Proc Natl Acad Sci U S A, 106,
16984-16989.
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PDB codes:
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C.Bauvois,
L.Jacquamet,
A.L.Huston,
F.Borel,
G.Feller,
and
J.L.Ferrer
(2008).
Crystal structure of the cold-active aminopeptidase from Colwellia psychrerythraea, a close structural homologue of the human bifunctional leukotriene A4 hydrolase.
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J Biol Chem, 283,
23315-23325.
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PDB code:
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C.L.Goonasekara,
and
D.H.Heeley
(2008).
Conformational properties of striated muscle tropomyosins from some salmonid fishes.
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J Muscle Res Cell Motil, 29,
135-143.
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J.C.Marx,
J.Poncin,
J.P.Simorre,
P.W.Ramteke,
and
G.Feller
(2008).
The noncatalytic triad of alpha-amylases: a novel structural motif involved in conformational stability.
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Proteins, 70,
320-328.
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O.Almog,
A.Kogan,
M.Leeuw,
G.Y.Gdalevsky,
R.Cohen-Luria,
and
A.H.Parola
(2008).
Structural insights into cold inactivation of tryptophanase and cold adaptation of subtilisin S41.
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Biopolymers, 89,
354-359.
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S.Ravaud,
X.Robert,
H.Watzlawick,
R.Haser,
R.Mattes,
and
N.Aghajari
(2007).
Trehalulose synthase native and carbohydrate complexed structures provide insights into sucrose isomerization.
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J Biol Chem, 282,
28126-28136.
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PDB codes:
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S.Srimathi,
G.Jayaraman,
G.Feller,
B.Danielsson,
and
P.R.Narayanan
(2007).
Intrinsic halotolerance of the psychrophilic alpha-amylase from Pseudoalteromonas haloplanktis.
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Extremophiles, 11,
505-515.
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V.Spiwok,
P.Lipovová,
T.Skálová,
J.Dusková,
J.Dohnálek,
J.Hasek,
N.J.Russell,
and
B.Králová
(2007).
Cold-active enzymes studied by comparative molecular dynamics simulation.
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J Mol Model, 13,
485-497.
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O.A.Adekoya,
R.Helland,
N.P.Willassen,
and
I.Sylte
(2006).
Comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family.
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Proteins, 62,
435-449.
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J.Arnórsdóttir,
M.M.Kristjánsson,
and
R.Ficner
(2005).
Crystal structure of a subtilisin-like serine proteinase from a psychrotrophic Vibrio species reveals structural aspects of cold adaptation.
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FEBS J, 272,
832-845.
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PDB codes:
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K.S.Siddiqui,
A.Poljak,
M.Guilhaus,
G.Feller,
S.D'Amico,
C.Gerday,
and
R.Cavicchioli
(2005).
Role of disulfide bridges in the activity and stability of a cold-active alpha-amylase.
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J Bacteriol, 187,
6206-6212.
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M.R.Smith,
and
J.C.Zahnley
(2005).
Characteristics of the amylase of Arthrobacter psychrolactophilus.
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J Ind Microbiol Biotechnol, 32,
439-448.
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A.Hoyoux,
V.Blaise,
T.Collins,
S.D'Amico,
E.Gratia,
A.L.Huston,
J.C.Marx,
G.Sonan,
Y.Zeng,
G.Feller,
and
C.Gerday
(2004).
Extreme catalysts from low-temperature environments.
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J Biosci Bioeng, 98,
317-330.
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A.Linden,
and
M.Wilmanns
(2004).
Adaptation of class-13 alpha-amylases to diverse living conditions.
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Chembiochem, 5,
231-239.
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D.Georlette,
V.Blaise,
T.Collins,
S.D'Amico,
E.Gratia,
A.Hoyoux,
J.C.Marx,
G.Sonan,
G.Feller,
and
C.Gerday
(2004).
Some like it cold: biocatalysis at low temperatures.
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FEMS Microbiol Rev, 28,
25-42.
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E.Bae,
and
G.N.Phillips
(2004).
Structures and analysis of highly homologous psychrophilic, mesophilic, and thermophilic adenylate kinases.
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J Biol Chem, 279,
28202-28208.
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PDB codes:
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H.Tsuruta,
J.Tamura,
H.Yamagata,
and
Y.Aizono
(2004).
Specification of amino acid residues essential for the catalytic reaction of cold-active protein-tyrosine phosphatase of a psychrophile, Shewanella sp.
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Biosci Biotechnol Biochem, 68,
440-443.
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M.Tehei,
B.Franzetti,
D.Madern,
M.Ginzburg,
B.Z.Ginzburg,
M.T.Giudici-Orticoni,
M.Bruschi,
and
G.Zaccai
(2004).
Adaptation to extreme environments: macromolecular dynamics in bacteria compared in vivo by neutron scattering.
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EMBO Rep, 5,
66-70.
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F.Van Petegem,
T.Collins,
M.A.Meuwis,
C.Gerday,
G.Feller,
and
J.Van Beeumen
(2003).
The structure of a cold-adapted family 8 xylanase at 1.3 A resolution. Structural adaptations to cold and investgation of the active site.
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J Biol Chem, 278,
7531-7539.
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PDB codes:
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G.Feller,
and
C.Gerday
(2003).
Psychrophilic enzymes: hot topics in cold adaptation.
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Nat Rev Microbiol, 1,
200-208.
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H.Orikoshi,
N.Baba,
S.Nakayama,
H.Kashu,
K.Miyamoto,
M.Yasuda,
Y.Inamori,
and
H.Tsujibo
(2003).
Molecular analysis of the gene encoding a novel cold-adapted chitinase (ChiB) from a marine bacterium, Alteromonas sp. strain O-7.
|
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J Bacteriol, 185,
1153-1160.
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J.Le Nours,
C.Ryttersgaard,
L.Lo Leggio,
P.R.Østergaard,
T.V.Borchert,
L.L.Christensen,
and
S.Larsen
(2003).
Structure of two fungal beta-1,4-galactanases: searching for the basis for temperature and pH optimum.
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Protein Sci, 12,
1195-1204.
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PDB codes:
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N.Aghajari,
F.Van Petegem,
V.Villeret,
J.P.Chessa,
C.Gerday,
R.Haser,
and
J.Van Beeumen
(2003).
Crystal structures of a psychrophilic metalloprotease reveal new insights into catalysis by cold-adapted proteases.
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Proteins, 50,
636-647.
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PDB codes:
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S.D'Amico,
J.C.Marx,
C.Gerday,
and
G.Feller
(2003).
Activity-stability relationships in extremophilic enzymes.
|
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J Biol Chem, 278,
7891-7896.
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X.Robert,
R.Haser,
T.E.Gottschalk,
F.Ratajczak,
H.Driguez,
B.Svensson,
and
N.Aghajari
(2003).
The structure of barley alpha-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs.
|
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Structure, 11,
973-984.
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PDB codes:
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C.Alquati,
L.De Gioia,
G.Santarossa,
L.Alberghina,
P.Fantucci,
and
M.Lotti
(2002).
The cold-active lipase of Pseudomonas fragi. Heterologous expression, biochemical characterization and molecular modeling.
|
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Eur J Biochem, 269,
3321-3328.
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G.Gianese,
F.Bossa,
and
S.Pascarella
(2002).
Comparative structural analysis of psychrophilic and meso- and thermophilic enzymes.
|
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Proteins, 47,
236-249.
|
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H.Tsuruta,
B.Mikami,
C.Yamamoto,
and
Y.Aizono
(2002).
Crystallization and preliminary X-ray studies of cold-active protein-tyrosine phosphatase of Shewanella sp.
|
| |
Acta Crystallogr D Biol Crystallogr, 58,
1465-1466.
|
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J.Arnórsdottir,
R.B.Smáradóttir,
O.T.Magnússon,
S.H.Thorbjarnardóttir,
G.Eggertsson,
and
M.M.Kristjánsson
(2002).
Characterization of a cloned subtilisin-like serine proteinase from a psychrotrophic Vibrio species.
|
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Eur J Biochem, 269,
5536-5546.
|
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L.K.Skov,
O.Mirza,
D.Sprogøe,
I.Dar,
M.Remaud-Simeon,
C.Albenne,
P.Monsan,
and
M.Gajhede
(2002).
Oligosaccharide and sucrose complexes of amylosucrase. Structural implications for the polymerase activity.
|
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J Biol Chem, 277,
47741-47747.
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PDB codes:
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M.L.Tutino,
E.Parrilli,
L.Giaquinto,
A.Duilio,
G.Sannia,
G.Feller,
and
G.Marino
(2002).
Secretion of alpha-amylase from Pseudoalteromonas haloplanktis TAB23: two different pathways in different hosts.
|
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J Bacteriol, 184,
5814-5817.
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N.Aghajari,
G.Feller,
C.Gerday,
and
R.Haser
(2002).
Structural basis of alpha-amylase activation by chloride.
|
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Protein Sci, 11,
1435-1441.
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PDB codes:
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S.D'Amico,
C.Gerday,
and
G.Feller
(2002).
Dual effects of an extra disulfide bond on the activity and stability of a cold-adapted alpha-amylase.
|
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J Biol Chem, 277,
46110-46115.
|
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S.D'Amico,
P.Claverie,
T.Collins,
D.Georlette,
E.Gratia,
A.Hoyoux,
M.A.Meuwis,
G.Feller,
and
C.Gerday
(2002).
Molecular basis of cold adaptation.
|
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Philos Trans R Soc Lond B Biol Sci, 357,
917-925.
|
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T.Murakawa,
H.Yamagata,
H.Tsuruta,
and
Y.Aizono
(2002).
Cloning of cold-active alkaline phosphatase gene of a psychrophile, Shewanella sp., and expression of the recombinant enzyme.
|
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Biosci Biotechnol Biochem, 66,
754-761.
|
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A.M.Brzozowski,
D.M.Lawson,
J.P.Turkenburg,
H.Bisgaard-Frantzen,
A.Svendsen,
T.V.Borchert,
Z.Dauter,
K.S.Wilson,
and
G.J.Davies
(2000).
Structural analysis of a chimeric bacterial alpha-amylase. High-resolution analysis of native and ligand complexes.
|
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Biochemistry, 39,
9099-9107.
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PDB codes:
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A.T.Bull,
A.C.Ward,
and
M.Goodfellow
(2000).
Search and discovery strategies for biotechnology: the paradigm shift.
|
| |
Microbiol Mol Biol Rev, 64,
573-606.
|
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|
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C.Gerday,
M.Aittaleb,
M.Bentahir,
J.P.Chessa,
P.Claverie,
T.Collins,
S.D'Amico,
J.Dumont,
G.Garsoux,
D.Georlette,
A.Hoyoux,
T.Lonhienne,
M.A.Meuwis,
and
G.Feller
(2000).
Cold-adapted enzymes: from fundamentals to biotechnology.
|
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Trends Biotechnol, 18,
103-107.
|
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D.Georlette,
Z.O.Jónsson,
F.Van Petegem,
J.Chessa,
J.Van Beeumen,
U.Hübscher,
and
C.Gerday
(2000).
A DNA ligase from the psychrophile Pseudoalteromonas haloplanktis gives insights into the adaptation of proteins to low temperatures.
|
| |
Eur J Biochem, 267,
3502-3512.
|
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H.K.Leiros,
N.P.Willassen,
and
A.O.Smalås
(2000).
Structural comparison of psychrophilic and mesophilic trypsins. Elucidating the molecular basis of cold-adaptation.
|
| |
Eur J Biochem, 267,
1039-1049.
|
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M.Rina,
C.Pozidis,
K.Mavromatis,
M.Tzanodaskalaki,
M.Kokkinidis,
and
V.Bouriotis
(2000).
Alkaline phosphatase from the Antarctic strain TAB5. Properties and psychrophilic adaptations.
|
| |
Eur J Biochem, 267,
1230-1238.
|
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A.Galkin,
L.Kulakova,
H.Ashida,
Y.Sawa,
and
N.Esaki
(1999).
Cold-adapted alanine dehydrogenases from two antarctic bacterial strains: gene cloning, protein characterization, and comparison with mesophilic and thermophilic counterparts.
|
| |
Appl Environ Microbiol, 65,
4014-4020.
|
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D.Maes,
J.P.Zeelen,
N.Thanki,
N.Beaucamp,
M.Alvarez,
M.H.Thi,
J.Backmann,
J.A.Martial,
L.Wyns,
R.Jaenicke,
and
R.K.Wierenga
(1999).
The crystal structure of triosephosphate isomerase (TIM) from Thermotoga maritima: a comparative thermostability structural analysis of ten different TIM structures.
|
| |
Proteins, 37,
441-453.
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PDB code:
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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
