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PDBsum entry 1thm
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Hydrolase(serine protease)
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PDB id
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1thm
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* Residue conservation analysis
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Enzyme class:
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E.C.3.4.21.66
- thermitase.
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Reaction:
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Hydrolysis of proteins, including collagen.
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J Mol Biol
214:261-279
(1990)
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PubMed id:
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Crystal structure of thermitase at 1.4 A resolution.
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A.V.Teplyakov,
I.P.Kuranova,
E.H.Harutyunyan,
B.K.Vainshtein,
C.Frömmel,
W.E.Höhne,
K.S.Wilson.
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ABSTRACT
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The crystal structure of thermitase, a subtilisin-type serine proteinase from
Thermoactinomyces vulgaris, was determined by X-ray diffraction at 1.4 A
resolution. The structure was solved by a combination of molecular and
isomorphous replacement. The starting model was that of subtilisin BPN' from the
Protein Data Bank, determined at 2.5 A resolution. The high-resolution
refinement was based on data collected using synchrotron radiation with a Fuji
image plate as detector. The model of thermitase refined to a conventional R
factor of 14.9% and contains 1997 protein atoms, 182 water molecules and two Ca
ions. The tertiary structure of thermitase is similar to that of the other
subtilisins although there are some significant differences in detail.
Comparison with subtilisin BPN' revealed two major structural differences. The
N-terminal region in thermitase, which is absent in subtilisin BPN', forms a
number of contacts with the tight Ca2+ binding site and indeed provides the very
tight binding of the Ca ion. In thermitase the loop of residues 60 to 65 forms
an additional (10) beta-strand of the central beta-sheet and the second Ca2+
binding site that has no equivalent in the subtilisin BPN' structure. The
observed differences in the Ca2+ binding and the increased number of ionic and
aromatic interactions in thermitase are likely sources of the enhanced stability
of thermitase.
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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.Tiberti,
and
E.Papaleo
(2011).
Dynamic properties of extremophilic subtilisin-like serine-proteases.
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J Struct Biol,
174,
69-83.
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G.D.Jones,
R.C.Le Pla,
and
P.B.Farmer
(2010).
Phosphotriester adducts (PTEs): DNA's overlooked lesion.
|
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Mutagenesis,
25,
3.
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G.Cheng,
P.Zhao,
X.F.Tang,
and
B.Tang
(2009).
Identification and characterization of a novel spore-associated subtilase from Thermoactinomyces sp. CDF.
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Microbiology,
155,
3661-3672.
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H.Fazelinia,
P.C.Cirino,
and
C.D.Maranas
(2009).
OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold.
|
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Protein Sci,
18,
180-195.
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O.Almog,
A.González,
N.Godin,
M.de Leeuw,
M.J.Mekel,
D.Klein,
S.Braun,
G.Shoham,
and
R.L.Walter
(2009).
The crystal structures of the psychrophilic subtilisin S41 and the mesophilic subtilisin Sph reveal the same calcium-loaded state.
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Proteins,
74,
489-496.
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PDB codes:
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A.I.Papisova,
S.A.Semenova,
I.u.A.Kislitsyn,
and
G.N.Rudenskaia
(2008).
[Characteristics of substrate hydrolysis by endopeptidases from the hepatopancreas of the king crab]
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Bioorg Khim,
34,
479-486.
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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.Q.Liu,
Z.H.Meng,
J.K.Yang,
Y.X.Fu,
and
K.Q.Zhang
(2007).
Characterizing structural features of cuticle-degrading proteases from fungi by molecular modeling.
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BMC Struct Biol,
7,
33.
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Y.Huang,
Y.Zhou,
W.Yang,
R.Butters,
H.W.Lee,
S.Li,
A.Castiblanco,
E.M.Brown,
and
J.J.Yang
(2007).
Identification and dissection of Ca(2+)-binding sites in the extracellular domain of Ca(2+)-sensing receptor.
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J Biol Chem,
282,
19000-19010.
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A.N.Larsen,
E.Moe,
R.Helland,
D.R.Gjellesvik,
and
N.P.Willassen
(2006).
Characterization of a recombinantly expressed proteinase K-like enzyme from a psychrotrophic Serratia sp.
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FEBS J,
273,
47-60.
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M.Pulido,
K.Saito,
S.Tanaka,
Y.Koga,
M.Morikawa,
K.Takano,
and
S.Kanaya
(2006).
Ca2+-dependent maturation of subtilisin from a hyperthermophilic archaeon, Thermococcus kodakaraensis: the propeptide is a potent inhibitor of the mature domain but is not required for its folding.
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Appl Environ Microbiol,
72,
4154-4162.
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R.Helland,
A.N.Larsen,
A.O.Smalås,
and
N.P.Willassen
(2006).
The 1.8 A crystal structure of a proteinase K-like enzyme from a psychrotroph Serratia species.
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FEBS J,
273,
61-71.
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PDB code:
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D.Segal,
and
M.Eisenstein
(2005).
The effect of resolution-dependent global shape modifications on rigid-body protein-protein docking.
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Proteins,
59,
580-591.
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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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M.E.Than,
S.Henrich,
G.P.Bourenkov,
H.D.Bartunik,
R.Huber,
and
W.Bode
(2005).
The endoproteinase furin contains two essential Ca2+ ions stabilizing its N-terminus and the unique S1 specificity pocket.
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Acta Crystallogr D Biol Crystallogr,
61,
505-512.
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A.Berchanski,
B.Shapira,
and
M.Eisenstein
(2004).
Hydrophobic complementarity in protein-protein docking.
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Proteins,
56,
130-142.
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C.H.Lee,
J.W.Jung,
A.Yee,
C.H.Arrowsmith,
and
W.Lee
(2004).
Solution structure of a novel calcium binding protein, MTH1880, from Methanobacterium thermoautotrophicum.
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Protein Sci,
13,
1148-1154.
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PDB codes:
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J.Wu,
Y.Bian,
B.Tang,
X.Chen,
P.Shen,
and
Z.Peng
(2004).
Cloning and analysis of WF146 protease, a novel thermophilic subtilisin-like protease with four inserted surface loops.
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FEMS Microbiol Lett,
230,
251-258.
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A.Heifetz,
E.Katchalski-Katzir,
and
M.Eisenstein
(2002).
Electrostatics in protein-protein docking.
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Protein Sci,
11,
571-587.
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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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O.V.Tsodikov,
M.T.Record,
and
Y.V.Sergeev
(2002).
Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature.
|
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J Comput Chem,
23,
600-609.
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W.Yang,
H.W.Lee,
H.Hellinga,
and
J.J.Yang
(2002).
Structural analysis, identification, and design of calcium-binding sites in proteins.
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Proteins,
47,
344-356.
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C.Vieille,
and
G.J.Zeikus
(2001).
Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability.
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Microbiol Mol Biol Rev,
65,
1.
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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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M.M.Kristjánsson,
O.T.Magnússon,
H.M.Gudmundsson,
G.A.Alfredsson,
and
H.Matsuzawa
(1999).
Properties of a subtilisin-like proteinase from a psychrotrophic Vibrio species comparison with proteinase K and aqualysin I.
|
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Eur J Biochem,
260,
752-760.
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G.Dong,
C.Vieille,
A.Savchenko,
and
J.G.Zeikus
(1997).
Cloning, sequencing, and expression of the gene encoding extracellular alpha-amylase from Pyrococcus furiosus and biochemical characterization of the recombinant enzyme.
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Appl Environ Microbiol,
63,
3569-3576.
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G.Feller,
Z.Zekhnini,
J.Lamotte-Brasseur,
and
C.Gerday
(1997).
Enzymes from cold-adapted microorganisms. The class C beta-lactamase from the antarctic psychrophile Psychrobacter immobilis A5.
|
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Eur J Biochem,
244,
186-191.
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H.Nakamura
(1996).
Roles of electrostatic interaction in proteins.
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Q Rev Biophys,
29,
1.
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M.Gerstein,
and
C.Chothia
(1996).
Packing at the protein-water interface.
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Proc Natl Acad Sci U S A,
93,
10167-10172.
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M.L.Remerowski,
H.A.Pepermans,
C.W.Hilbers,
and
F.J.Van De Ven
(1996).
Backbone dynamics of the 269-residue protease Savinase determined from 15N-NMR relaxation measurements.
|
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Eur J Biochem,
235,
629-640.
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M.Hennig,
B.Darimont,
R.Sterner,
K.Kirschner,
and
J.N.Jansonius
(1995).
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,
3,
1295-1306.
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PDB code:
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G.Feller,
F.Payan,
F.Theys,
M.Qian,
R.Haser,
and
C.Gerday
(1994).
Stability and structural analysis of alpha-amylase from the antarctic psychrophile Alteromonas haloplanctis A23.
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Eur J Biochem,
222,
441-447.
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G.Lange,
C.Betzel,
S.Branner,
and
K.S.Wilson
(1994).
Crystallographic studies of Savinase, a subtilisin-like proteinase, at pH 10.5.
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Eur J Biochem,
224,
507-518.
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P.Völkl,
P.Markiewicz,
K.O.Stetter,
and
J.H.Miller
(1994).
The sequence of a subtilisin-type protease (aerolysin) from the hyperthermophilic archaeum Pyrobaculum aerophilum reveals sites important to thermostability.
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Protein Sci,
3,
1329-1340.
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R.J.Siezen,
J.W.Creemers,
and
W.J.Van de Ven
(1994).
Homology modelling of the catalytic domain of human furin. A model for the eukaryotic subtilisin-like proprotein convertases.
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Eur J Biochem,
222,
255-266.
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A.Teplyakov,
K.Polyakov,
G.Obmolova,
B.Strokopytov,
I.Kuranova,
A.Osterman,
N.Grishin,
S.Smulevitch,
O.Zagnitko,
and
O.Galperina
(1992).
Crystal structure of carboxypeptidase T from Thermoactinomyces vulgaris.
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Eur J Biochem,
208,
281-288.
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PDB code:
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P.Gros,
A.V.Teplyakov,
and
W.G.Hol
(1992).
Effects of eglin-c binding to thermitase: three-dimensional structure comparison of native thermitase and thermitase eglin-c complexes.
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Proteins,
12,
63-74.
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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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Links
