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PDBsum entry 1lxm
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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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Structure and flexibility of streptococcus agalactiae hyaluronate lyase complex with its substrate. Insights into the mechanism of processive degradation of hyaluronan.
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Authors
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L.V.Mello,
B.L.De groot,
S.Li,
M.J.Jedrzejas.
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Ref.
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J Biol Chem, 2002,
277,
36678-36688.
[DOI no: ]
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PubMed id
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Abstract
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Streptococcus agalactiae hyaluronate lyase degrades primarily hyaluronan, the
main polysaccharide component of the host connective tissues, into unsaturated
disaccharide units as the end product. Such function of the enzyme destroys the
normal connective tissue structure of the host and exposes the tissue cells to
various bacterial toxins. The crystal structure of hexasaccharide hyaluronan
complex with the S. agalactiae hyaluronate lyase was determined at 2.2 A
resolution; the mechanism of the catalytic process, including the identification
of specific residues involved in the degradation of hyaluronan, was clearly
identified. The enzyme is composed structurally and functionally from two
distinct domains, an alpha-helical alpha-domain and a beta-sheet beta-domain.
The flexibility of the protein was investigated by comparing the crystal
structures of the S. agalactiae and the Streptococcus pneumoniae enzymes, and by
using essential dynamics analyses of CONCOORD computer simulations. These
revealed important modes of flexibility, which could be related to the protein
function. First, a rotation/twist of the alpha-domain relative to the
beta-domain is potentially related to the mechanism of processivity of the
enzyme; this twist motion likely facilitates shifting of the ligand along the
catalytic site cleft in order to reposition it to be ready for further cleavage.
Second, a movement of the alpha- and beta-domains with respect to each other was
found to contribute to a change in electrostatic characteristics of the enzyme
and appears to facilitate binding of the negatively charged hyaluronan ligand.
Third, an opening/closing of the substrate binding cleft brings a catalytic
histidine closer to the cleavable substrate beta1,4-glycosidic bond. This
opening/closing mode also reflects the main conformational difference between
the crystal structures of the S. agalactiae and the S. pneumoniae hyaluronate
lyases.
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Figure 1.
Fig. 1. The structure of S. agalactiae hyaluronate lyase
with bound hexasaccharide hyaluronan substrate. A, ribbon
drawing of the structure of the complex. All three domains of
the enzyme are shown, the N-terminal  -sheet
domain ( II-domain,
top), the  -helical
domain ( -domain,
middle), the C-terminal -sheet
domain ( II-domain,
bottom), as well as the cleft with the bound hexasaccharide unit
of hyaluronan substrate (depicted in a ball and stick fashion
with bonds colored in red). The structure of the enzyme is
color-coded by the secondary structure elements ( -helices in
blue, 3[10] helices in purple, -sheets in
green), and the atoms of the substrate are colored by the atom
type (carbon atoms in green, oxygen atoms in red, and nitrogen
atoms in blue). Consecutive disaccharide units of HA starting
from the reducing end are labeled as HA1 , HA2, and HA3. B,
comparison of structures of S. agalactiae and S. pneumoniae
hyaluronate lyases. The S. agalactiae enzyme (black) (domains
labeled) has an additional domain at its N terminus ( I-domain).
The cleft area in this enzyme is also wider than that of the S.
pneumoniae hyaluronate lyase (blue) (maximum difference in width
of ~7 Å). C, electrostatic potential distribution in the
catalytic cleft. The positive potential is shown in blue and the
negative potential in red. The majority of the cleft is highly
positively charged (middle and the left side; positive patch)
whereas at the product-releasing end of the cleft is negatively
charged (right side of the cleft; a negative patch). The
hydrophobic patch is also shown. Bound hexasaccharide hyaluronan
is shown as sticks color-coded by atom type. Reducing and
non-reducing ends of HA are labeled.
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Figure 3.
Fig. 3. DynDom analysis of the difference between the S.
pneumoniae and S. agalactiae hyaluronate lyase x-ray crystal
structures. Shown is the x-ray structure of S. agalactiae HL,
with the yellow arrow depicting the rotation axis for the domain
transition toward the S. pneumoniae HL structure, in which the
red domain rotates with respect to the blue domain. The domain
motion corresponds to a closure motion (white arrows). The green
residues provide the flexible linker between the two domains.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2002,
277,
36678-36688)
copyright 2002.
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