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PDBsum entry 2mef
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* Residue conservation analysis
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Enzyme class:
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E.C.3.2.1.17
- lysozyme.
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Reaction:
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Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.
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Protein Eng
12:841-850
(1999)
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PubMed id:
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Contribution of amino acid substitutions at two different interior positions to the conformational stability of human lysozyme.
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J.Funahashi,
K.Takano,
Y.Yamagata,
K.Yutani.
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ABSTRACT
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To elucidate correlative relationships between structural change and
thermodynamic stability in proteins, a series of mutant human lysozymes modified
at two buried positions (Ile56 and Ile59) were examined. Their thermodynamic
parameters of denaturation and crystal structures were studied by calorimetry
and X-ray crystallography. The mutants at positions 56 and 59 exhibited
different responses to a series of amino acid substitutions. The changes in
stability due to substitutions showed a linear correlation with changes in
hydrophobicity of substituted residues, having different slopes at each mutation
site. However, the stability of each mutant was found to be represented by a
unique equation involving physical properties calculated from mutant structures.
By fitting present and previous stability data for mutant human lysozymes
substituted at various positions to the equation, the magnitudes of the
hydrophobicity of a carbon atom and the hydrophobicity of nitrogen and neutral
oxygen atoms were found to be 0.178 and -0.013 kJ/mol.A(2), respectively. It was
also found that the contribution of a hydrogen bond with a length of 3.0 A to
protein stability was 5.1 kJ/mol and the entropy loss of newly introduction of a
water molecules was 7.8 kJ/mol.
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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.Wohlkönig,
J.Huet,
Y.Looze,
and
R.Wintjens
(2010).
Structural relationships in the lysozyme superfamily: significant evidence for glycoside hydrolase signature motifs.
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PLoS One,
5,
e15388.
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C.L.Hagan,
R.J.Johnson,
A.Dhulesia,
M.Dumoulin,
J.Dumont,
E.De Genst,
J.Christodoulou,
C.V.Robinson,
C.M.Dobson,
and
J.R.Kumita
(2010).
A non-natural variant of human lysozyme (I59T) mimics the in vitro behaviour of the I56T variant that is responsible for a form of familial amyloidosis.
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Protein Eng Des Sel,
23,
499-506.
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H.Yamamoto,
K.Takio,
M.Sugahara,
and
N.Kunishima
(2008).
Structure of a haloacid dehalogenase superfamily phosphatase PH1421 from Pyrococcus horikoshii OT3: oligomeric state and thermoadaptation mechanism.
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Acta Crystallogr D Biol Crystallogr,
64,
1068-1077.
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PDB code:
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K.Shimizu,
C.Kuroishi,
M.Sugahara,
and
N.Kunishima
(2008).
Structure of peptidyl-tRNA hydrolase 2 from Pyrococcus horikoshii OT3: insight into the functional role of its dimeric state.
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Acta Crystallogr D Biol Crystallogr,
64,
444-453.
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PDB codes:
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L.Fernández,
J.Caballero,
J.I.Abreu,
and
M.Fernández
(2007).
Amino acid sequence autocorrelation vectors and Bayesian-regularized genetic neural networks for modeling protein conformational stability: gene V protein mutants.
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Proteins,
67,
834-852.
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J.R.Kumita,
R.J.Johnson,
M.J.Alcocer,
M.Dumoulin,
F.Holmqvist,
M.G.McCammon,
C.V.Robinson,
D.B.Archer,
and
C.M.Dobson
(2006).
Impact of the native-state stability of human lysozyme variants on protein secretion by Pichia pastoris.
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FEBS J,
273,
711-720.
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M.Sugahara,
N.Ohshima,
Y.Ukita,
M.Sugahara,
and
N.Kunishima
(2005).
Structure of ATP-dependent phosphoenolpyruvate carboxykinase from Thermus thermophilus HB8 showing the structural basis of induced fit and thermostability.
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Acta Crystallogr D Biol Crystallogr,
61,
1500-1507.
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PDB codes:
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H.Takahashi,
E.Inagaki,
Y.Fujimoto,
C.Kuroishi,
Y.Nodake,
Y.Nakamura,
F.Arisaka,
K.Yutani,
S.Kuramitsu,
S.Yokoyama,
M.Yamamoto,
M.Miyano,
and
T.H.Tahirov
(2004).
Structure and implications for the thermal stability of phosphopantetheine adenylyltransferase from Thermus thermophilus.
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Acta Crystallogr D Biol Crystallogr,
60,
97.
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PDB code:
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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.L.Lomize,
M.Y.Reibarkh,
and
I.D.Pogozheva
(2002).
Interatomic potentials and solvation parameters from protein engineering data for buried residues.
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Protein Sci,
11,
1984-2000.
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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.Zhou,
and
Y.Zhou
(2002).
Stability scale and atomic solvation parameters extracted from 1023 mutation experiments.
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Proteins,
49,
483-492.
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K.Takano,
J.Funahashi,
and
K.Yutani
(2001).
The stability and folding process of amyloidogenic mutant human lysozymes.
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Eur J Biochem,
268,
155-159.
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K.Takano,
Y.Yamagata,
and
K.Yutani
(2001).
Role of non-glycine residues in left-handed helical conformation for the conformational stability of human lysozyme.
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Proteins,
44,
233-243.
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PDB codes:
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K.Takano,
Y.Yamagata,
and
K.Yutani
(2001).
Role of amino acid residues in left-handed helical conformation for the conformational stability of a protein.
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Proteins,
45,
274-280.
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PDB codes:
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K.Takano,
Y.Yamagata,
and
K.Yutani
(2001).
Contribution of polar groups in the interior of a protein to the conformational stability.
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Biochemistry,
40,
4853-4858.
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PDB codes:
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J.Funahashi,
K.Takano,
Y.Yamagata,
and
K.Yutani
(2000).
Role of surface hydrophobic residues in the conformational stability of human lysozyme at three different positions.
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Biochemistry,
39,
14448-14456.
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PDB codes:
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K.Takano,
K.Tsuchimori,
Y.Yamagata,
and
K.Yutani
(2000).
Contribution of salt bridges near the surface of a protein to the conformational stability.
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Biochemistry,
39,
12375-12381.
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PDB codes:
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K.Takano,
Y.Yamagata,
and
K.Yutani
(2000).
Role of amino acid residues at turns in the conformational stability and folding of human lysozyme.
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Biochemistry,
39,
8655-8665.
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PDB codes:
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S.T.Thomas,
and
G.I.Makhatadze
(2000).
Contribution of the 30/36 hydrophobic contact at the C-terminus of the alpha-helix to the stability of the ubiquitin molecule.
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Biochemistry,
39,
10275-10283.
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K.Takano,
K.Tsuchimori,
Y.Yamagata,
and
K.Yutani
(1999).
Effect of foreign N-terminal residues on the conformational stability of human lysozyme.
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Eur J Biochem,
266,
675-682.
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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
