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PDBsum entry 1svn
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Serine protease
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PDB id
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1svn
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.3.4.21.62
- subtilisin.
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Reaction:
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Hydrolysis of proteins with broad specificity for peptide bonds, and a preference for a large uncharged residue in P1. Hydrolyzes peptide amides.
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J Mol Biol
223:427-445
(1992)
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PubMed id:
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Crystal structure of the alkaline proteinase Savinase from Bacillus lentus at 1.4 A resolution.
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C.Betzel,
S.Klupsch,
G.Papendorf,
S.Hastrup,
S.Branner,
K.S.Wilson.
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ABSTRACT
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Savinase (EC3.4.21.14) is secreted by the alkalophilic bacterium Bacillus lentus
and is a representative of that subgroup of subtilisin enzymes with maximum
stability in the pH range 7 to 10 and high activity in the range 8 to 12. It is
therefore of major industrial importance for use in detergents. The crystal
structure of the native form of Savinase has been refined using X-ray
diffraction data to 1.4 A resolution. The starting model was that of subtilisin
Carlsberg. A comparison to the structures of the closely related subtilisins
Carlsberg and BPN' and to the more distant thermitase and proteinase K is
presented. The structure of Savinase is very similar to those of homologous
Bacillus subtilisins. There are two calcium ions in the structure, equivalent to
the strong and the weak calcium-binding sites in subtilisin Carlsberg and
subtilisin BPN', well known for their stabilizing effect on the subtilisins. The
structure of Savinase shows novel features that can be related to its stability
and activity. The relatively high number of salt bridges in Savinase is likely
to contribute to its high thermal stability. The non-conservative substitutions
and deletions in the hydrophobic binding pocket S1 result in the most
significant structural differences from the other subtilisins. The different
composition of the S1 binding loop as well as the more hydrophobic character of
the substrate-binding region probably contribute to the alkaline activity
profile of the enzyme. The model of Savinase contains 1880 protein atoms, 159
water molecules and two calcium ions. The crystallographic R-factor [formula;
see text].
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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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A.Sircar,
S.Chaudhury,
K.P.Kilambi,
M.Berrondo,
and
J.J.Gray
(2010).
A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19.
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Proteins,
78,
3115-3123.
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M.Eisenstein,
A.Ben-Shimon,
Z.Frankenstein,
and
N.Kowalsman
(2010).
CAPRI targets T29-T42: proving ground for new docking procedures.
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Proteins,
78,
3174-3181.
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S.Y.Huang,
and
X.Zou
(2010).
MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19.
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Proteins,
78,
3096-3103.
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K.Saeki,
K.Ozaki,
T.Kobayashi,
and
S.Ito
(2007).
Detergent alkaline proteases: enzymatic properties, genes, and crystal structures.
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J Biosci Bioeng,
103,
501-508.
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Y.Kageyama,
Y.Takaki,
S.Shimamura,
S.Nishi,
Y.Nogi,
K.Uchimura,
T.Kobayashi,
J.Hitomi,
K.Ozaki,
S.Kawai,
S.Ito,
and
K.Horikoshi
(2007).
Intragenomic diversity of the V1 regions of 16S rRNA genes in high-alkaline protease-producing Bacillus clausii spp.
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Extremophiles,
11,
597-603.
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Y.Takimura,
K.Saito,
M.Okuda,
Y.Kageyama,
K.Saeki,
K.Ozaki,
S.Ito,
and
T.Kobayashi
(2007).
Alkaliphilic Bacillus sp. strain KSM-LD1 contains a record number of subtilisin-like serine proteases genes.
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Appl Microbiol Biotechnol,
76,
395-405.
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Y.Oguchi,
H.Maeda,
K.Abe,
T.Nakajima,
T.Uchida,
and
Y.Yamagata
(2006).
Hydrophobic interactions between the secondary structures on the molecular surface reinforce the alkaline stability of serine protease.
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Biotechnol Lett,
28,
1383-1391.
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B.G.Davis,
R.F.Sala,
D.R.Hodgson,
A.Ullman,
K.Khumtaveeporn,
D.A.Estell,
K.Sanford,
R.R.Bott,
and
J.B.Jones
(2003).
Selective protein degradation by ligand-targeted enzymes: towards the creation of catalytic antagonists.
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Chembiochem,
4,
533-537.
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C.A.Voigt,
C.Martinez,
Z.G.Wang,
S.L.Mayo,
and
F.H.Arnold
(2002).
Protein building blocks preserved by recombination.
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Nat Struct Biol,
9,
553-558.
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Y.Yamagata,
H.Maeda,
T.Nakajima,
and
E.Ichishima
(2002).
The molecular surface of proteolytic enzymes has an important role in stability of the enzymatic activity in extraordinary environments.
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Eur J Biochem,
269,
4577-4585.
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T.Nonaka,
M.Fujihashi,
A.Kita,
K.Saeki,
S.Ito,
and
K.Miki
(2001).
Crystallization and preliminary X-ray diffraction studies of a novel alkaline serine protease (KP-43) from alkaliphilic Bacillus sp. strain KSM-KP43.
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Acta Crystallogr D Biol Crystallogr,
57,
717-718.
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P.N.Bryan
(2000).
Protein engineering of subtilisin.
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Biochim Biophys Acta,
1543,
203-222.
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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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V.S.Lamzin,
R.J.Morris,
Z.Dauter,
K.S.Wilson,
and
M.M.Teeter
(1999).
Experimental observation of bonding electrons in proteins.
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J Biol Chem,
274,
20753-20755.
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G.DeSantis,
P.Berglund,
M.R.Stabile,
M.Gold,
and
J.B.Jones
(1998).
Site-directed mutagenesis combined with chemical modification as a strategy for altering the specificity of the S1 and S1' pockets of subtilisin Bacillus lentus.
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Biochemistry,
37,
5968-5973.
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J.R.Martin,
F.A.Mulder,
Y.Karimi-Nejad,
J.van der Zwan,
M.Mariani,
D.Schipper,
and
R.Boelens
(1997).
The solution structure of serine protease PB92 from Bacillus alcalophilus presents a rigid fold with a flexible substrate-binding site.
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Structure,
5,
521-532.
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PDB code:
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A.Sättler,
S.Kanka,
K.H.Maurer,
and
D.Riesner
(1996).
Thermostable variants of subtilisin selected by temperature-gradient gel electrophoresis.
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Electrophoresis,
17,
784-792.
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J.J.Perona,
and
C.S.Craik
(1995).
Structural basis of substrate specificity in the serine proteases.
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Protein Sci,
4,
337-360.
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PDB code:
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M.R.Egmond,
W.P.Antheunisse,
C.M.van Bemmel,
P.Ravestein,
and
L.G.Frenken
(1995).
Structural and functional aspects of an industrial lipase.
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Ann N Y Acad Sci,
750,
195-201.
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S.L.Strausberg,
P.A.Alexander,
D.T.Gallagher,
G.L.Gilliland,
B.L.Barnett,
and
P.N.Bryan
(1995).
Directed evolution of a subtilisin with calcium-independent stability.
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Biotechnology (N Y),
13,
669-673.
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Y.Yamagata,
K.Isshiki,
and
E.Ichishima
(1995).
Subtilisin Sendai from alkalophilic Bacillus sp.: molecular and enzymatic properties of the enzyme and molecular cloning and characterization of the gene, aprS.
|
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Enzyme Microb Technol,
17,
653-663.
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Y.Yamagata,
T.Sato,
S.Hanzawa,
and
E.Ichishima
(1995).
The structure of subtilisin ALP I from alkalophilic Bacillus sp. NKS-21.
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Curr Microbiol,
30,
201-209.
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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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W.D.van Dongen,
J.H.van Bommel,
P.D.van Wassenaar,
W.Heerma,
and
J.Haverkamp
(1994).
Rapid identification of specific mutations in the sequence of an enzyme variant produced by protein engineering using high-performance liquid chromatographic/fast atom bombardment mass spectrometric techniques.
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Biol Mass Spectrom,
23,
675-681.
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A.Sättler,
and
D.Riesner
(1993).
Temperature-gradient gel electrophoresis for analysis and screening of thermostable proteases.
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Electrophoresis,
14,
782-788.
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F.H.Arnold
(1993).
Protein engineering for unusual environments.
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Curr Opin Biotechnol,
4,
450-455.
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L.M.Bech,
S.B.Sørensen,
and
K.Breddam
(1992).
Mutational replacements in subtilisin 309. Val104 has a modulating effect on the P4 substrate preference.
|
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Eur J Biochem,
209,
869-874.
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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
