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PDBsum entry 1jkd
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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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DOI no:
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Protein Sci
6:473-476
(1997)
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PubMed id:
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Importance of van der Waals contact between Glu 35 and Trp 109 to the catalytic action of human lysozyme.
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M.Muraki,
S.Goda,
H.Nagahora,
K.Harata.
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ABSTRACT
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The importance of van der Waals contact between Glu 35 and Trp 109 to the
active-site structure and the catalytic properties of human lysozyme (HL) has
been investigated by site-directed mutagenesis. The X-ray analysis of mutant HLs
revealed that both the replacement of Glu 35 by Asp or Ala, and the replacement
of Trp 109 by Phe or Ala resulted in a significant but localized change in the
active-site cleft geometry. A prominent movement of the backbone structure was
detected in the region of residues 110 to 120 and in the region of residues 100
to 115 for the mutations concerning Glu 35 and Trp 109, respectively.
Accompanied by the displacement of the main-chain atoms with a maximal deviation
of C alpha atom position ranging from 0.7 A to 1.0 A, the mutant HLs showed a
remarkable change in the catalytic properties against Micrococcus luteus cell
substrate as compared with native HL. Although the replacement of Glu 35 by Ala
completely abolished the lytic activity, HL-Asp 35 mutant retained a weak but a
certain lytic activity, showing the possible involvement of the side-chain
carboxylate group of Asp 35 in the catalytic action. The kinetic consequence
derived from the replacement of Trp 109 by Phe or Ala together with the result
of the structural change suggested that the structural detail of the cleft lobe
composed of the residues 100 to 115 centered at Ala 108 was responsible for the
turnover in the reaction of HL against the bacterial cell wall substrate. The
results revealed that the van der Waals contact between Glu 35 and Trp 109 was
an essential determinant in the catalytic action of HL.
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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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J.S.Cantwell,
W.R.Novak,
P.F.Wang,
M.J.McLeish,
G.L.Kenyon,
and
P.C.Babbitt
(2001).
Mutagenesis of two acidic active site residues in human muscle creatine kinase: implications for the catalytic mechanism.
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Biochemistry,
40,
3056-3061.
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M.C.Vaney,
I.Broutin,
P.Retailleau,
A.Douangamath,
S.Lafont,
C.Hamiaux,
T.Prangé,
A.Ducruix,
and
M.Riès-Kautt
(2001).
Structural effects of monovalent anions on polymorphic lysozyme crystals.
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Acta Crystallogr D Biol Crystallogr,
57,
929-940.
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PDB codes:
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S.Mine,
T.Ueda,
Y.Hashimoto,
and
T.Imoto
(2000).
Analysis of the internal motion of free and ligand-bound human lysozyme by use of 15N NMR relaxation measurement: a comparison with those of hen lysozyme.
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Protein Sci,
9,
1669-1684.
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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
