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PDBsum entry 1g0q
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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 Sci
10:1067-1078
(2001)
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PubMed id:
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Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme.
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J.Xu,
W.A.Baase,
M.L.Quillin,
E.P.Baldwin,
B.W.Matthews.
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ABSTRACT
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To investigate the structural and thermodynamic basis of the binding of solvent
at internal sites within proteins a number of mutations were constructed in T4
lysozyme. Some of these were designed to introduce new solvent-binding sites.
Others were intended to displace solvent from preexisting sites. In one case
Val-149 was replaced with alanine, serine, cysteine, threonine, isoleucine, and
glycine. Crystallographic analysis shows that, with the exception of isoleucine,
each of these substitutions results in the binding of solvent at a polar site
that is sterically blocked in the wild-type enzyme. Mutations designed to
perturb or displace a solvent molecule present in the native enzyme included the
replacement of Thr-152 with alanine, serine, cysteine, valine, and isoleucine.
Although the solvent molecule was moved in some cases by up to 1.7 A, in no case
was it completely removed from the folded protein. The results suggest that
hydrogen bonds from the protein to bound solvent are energy neutral. The binding
of solvent to internal sites within proteins also appears to be energy neutral
except insofar as the bound solvent may prevent a loss of energy due to
potential hydrogen bonding groups that would otherwise be unsatisfied. The
introduction of a solvent-binding site appears to require not only a cavity to
accommodate the water molecule but also the presence of polar groups to help
satisfy its hydrogen-bonding potential. It may be easier to design a site to
accommodate two or more water molecules rather than one as the solvent molecules
can then hydrogen-bond to each other. For similar reasons it is often difficult
to design a point mutation that will displace a single solvent molecule from the
core of a protein.
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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.Madhumalar,
D.J.Smith,
and
C.Verma
(2008).
Stability of the core domain of p53: insights from computer simulations.
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BMC Bioinformatics,
9,
S17.
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C.Mattos,
and
A.C.Clark
(2008).
Minimizing frustration by folding in an aqueous environment.
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Arch Biochem Biophys,
469,
118-131.
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J.L.Schlessman,
C.Abe,
A.Gittis,
D.A.Karp,
M.A.Dolan,
and
B.García-Moreno E
(2008).
Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups.
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Biophys J,
94,
3208-3216.
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PDB codes:
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N.Ando,
B.Barstow,
W.A.Baase,
A.Fields,
B.W.Matthews,
and
S.M.Gruner
(2008).
Structural and thermodynamic characterization of T4 lysozyme mutants and the contribution of internal cavities to pressure denaturation.
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Biochemistry,
47,
11097-11109.
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Y.Wang,
S.Maegawa,
Y.Akiyama,
and
Y.Ha
(2007).
The role of L1 loop in the mechanism of rhomboid intramembrane protease GlpG.
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J Mol Biol,
374,
1104-1113.
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PDB codes:
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Z.Li,
and
T.Lazaridis
(2007).
Water at biomolecular binding interfaces.
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Phys Chem Chem Phys,
9,
573-581.
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J.W.Schymkowitz,
F.Rousseau,
I.C.Martins,
J.Ferkinghoff-Borg,
F.Stricher,
and
L.Serrano
(2005).
Prediction of water and metal binding sites and their affinities by using the Fold-X force field.
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Proc Natl Acad Sci U S A,
102,
10147-10152.
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M.K.Yadav,
J.E.Redman,
L.J.Leman,
J.M.Alvarez-Gutiérrez,
Y.Zhang,
C.D.Stout,
and
M.R.Ghadiri
(2005).
Structure-based engineering of internal cavities in coiled-coil peptides.
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Biochemistry,
44,
9723-9732.
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PDB codes:
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S.D.Sharrow,
K.A.Edmonds,
M.A.Goodman,
M.V.Novotny,
and
M.J.Stone
(2005).
Thermodynamic consequences of disrupting a water-mediated hydrogen bond network in a protein:pheromone complex.
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Protein Sci,
14,
249-256.
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S.Park,
and
J.G.Saven
(2005).
Statistical and molecular dynamics studies of buried waters in globular proteins.
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Proteins,
60,
450-463.
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B.H.Mooers,
and
B.W.Matthews
(2004).
Use of an ion-binding site to bypass the 1000-atom limit to structure determination by direct methods.
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Acta Crystallogr D Biol Crystallogr,
60,
1726-1737.
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PDB codes:
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S.Vaitheeswaran,
H.Yin,
J.C.Rasaiah,
and
G.Hummer
(2004).
Water clusters in nonpolar cavities.
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Proc Natl Acad Sci U S A,
101,
17002-17005.
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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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B.Xu,
Q.X.Hua,
S.H.Nakagawa,
W.Jia,
Y.C.Chu,
P.G.Katsoyannis,
and
M.A.Weiss
(2002).
A cavity-forming mutation in insulin induces segmental unfolding of a surrounding alpha-helix.
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Protein Sci,
11,
104-116.
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PDB code:
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J.Mendes,
R.Guerois,
and
L.Serrano
(2002).
Energy estimation in protein design.
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Curr Opin Struct Biol,
12,
441-446.
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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
