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PDBsum entry 1qut
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structure of escherichia coli lytic transglycosylase slt35 reveals a lysozyme-Like catalytic domain with an ef-Hand.
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Authors
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E.J.Van asselt,
A.J.Dijkstra,
K.H.Kalk,
B.Takacs,
W.Keck,
B.W.Dijkstra.
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Ref.
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Structure, 1999,
7,
1167-1180.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: Lytic transglycosylases are bacterial muramidases that catalyse the
cleavage of the beta- 1,4-glycosidic bond between N-acetylmuramic acid (MurNAc)
and N-acetylglucosamine (GlcNAc) in peptidoglycan with concomitant formation of
a 1,6-anhydrobond in the MurNAc residue. These muramidases play an important
role in the metabolism of the bacterial cell wall and might therefore be
potential targets for the rational design of antibacterial drugs. One of the
lytic transglycosylases is Slt35, a naturally occurring soluble fragment of the
outer membrane bound lytic transglycosylase B (MltB) from Escherichia coli.
RESULTS: The crystal structure of Slt35 has been determined at 1.7 A resolution.
The structure reveals an ellipsoid molecule with three domains called the alpha,
beta and core domains. The core domain is sandwiched between the alpha and beta
domains. Its fold resembles that of lysozyme, but it contains a single metal ion
binding site in a helix-loop-helix module that is surprisingly similar to the
eukaryotic EF-hand calcium-binding fold. Interestingly, the Slt35 EF-hand loop
consists of 15 residues instead of the usual 12 residues. The only other
prokaryotic proteins with an EF-hand motif identified so far are the
D-galactose-binding proteins. Residues from the alpha and core domains form a
deep groove where the substrate fragment GlcNAc can be bound. CONCLUSIONS: The
three-domain structure of Slt35 is completely different from the Slt70
structure, the only other lytic transglycosylase of known structure.
Nevertheless, the core domain of Slt35 closely resembles the fold of the
catalytic domain of Slt70, despite the absence of any obvious sequence
similarity. Residue Glu162 of Slt35 is in an equivalent position to Glu478, the
catalytic acid/base of Slt70. GlcNAc binds close to Glu162 in the deep groove.
Moreover, mutation of Glu162 into a glutamine residue yielded a completely
inactive enzyme. These observations indicate the location of the active site and
strongly support a catalytic role for Glu162.
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Figure 3.
Figure 3. The metal ion binding sites in (a) Slt35 and (b)
carp parvalbumin B (PDB entry code 5cpv). (c,d) Superposition of
the metal ion binding sites in Slt35 and parvalbumin B. Part (c)
shows a close-up of the binding site, (d) shows the orientation
and position of the EF-hand helices in the two proteins.
Residues 90-98 of parvalbumin B (green) were superimposed on
residues 237-245 of Slt35 (blue) with an rmsd of 0.32 Å 2 for
nine Ca atoms. Residues of Slt35 that were not used in the
superposition are shown in yellow. Helices E and F (green)
belong to parvalbumin and the a helices H10 and H11 (yellow) are
from Slt35.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1999,
7,
1167-1180)
copyright 1999.
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Secondary reference #1
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Title
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Accelerated X-Ray structure elucidation of a 36 kda muramidase/transglycosylase using warp.
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Authors
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E.J.Van asselt,
A.Perrakis,
K.H.Kalk,
V.S.Lamzin,
B.W.Dijkstra.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1998,
54,
58-73.
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PubMed id
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