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PDBsum entry 1ee6
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* Residue conservation analysis
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Enzyme class:
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E.C.4.2.2.2
- pectate lyase.
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Pathway:
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Pectin and Pectate Lyases
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Reaction:
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Eliminative cleavage of pectate to give oligosaccharides with 4-deoxy- alpha-D-gluc-4-enuronosyl groups at their non-reducing ends.
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DOI no:
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Acta Crystallogr D Biol Crystallogr
57:1786-1792
(2001)
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PubMed id:
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The first structure of pectate lyase belonging to polysaccharide lyase family 3.
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M.Akita,
A.Suzuki,
T.Kobayashi,
S.Ito,
T.Yamane.
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ABSTRACT
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The crystal structure of a highly alkaline low molecular weight pectate lyase
(Pel-15) was determined at 1.5 A resolution by the multiple isomorphous
replacement (MIR) method. This is the first pectate lyase structure from
polysaccharide lyase family 3. The overall structure is a simple eight-turn
right-handed parallel beta-helix domain with one long loop protruding from one
side of the beta-helix. The low molecular weight of Pel-15 derives from the lack
of N- and C-terminal extensions that are found in many beta-helix proteins.
Although the structure has one calcium ion at pH 6.7, raising the pH to 9.5
results in the binding of an additional calcium ion. The common calcium ion
found in both the pH 6.5 and 9.5 structures seems to stabilize both the
beta-helix structure and the long protruding loop. The additional calcium ion
found in the pH 9.5 structure alone may neutralize the acidic substrate. The
region around the additional calcium ion is thought to bind to the substrate, as
this region is rich in charged amino-acid residues which are required in
catalysis.
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Selected figure(s)
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Figure 3.
Figure 3 Stereoview of the Pel-15 unique calcium-binding site
formed by Asp80, Val81, Lys103 and three water molecules. One
calcium-bound water molecule is bound to the O atom of Gly34 on
the first T3. The location of this region is shown in Fig. 1-.
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Figure 5.
Figure 5 Stereoviews of the T3-PB1 groove regions of (a) Pel-15
and (b) Ech-PelC (PDB entry [202]1air ). The location of this
region is shown in Fig. 1[203] [link]-[204][turqarr.gif] .
Amino-acid side chains are represented by stick models. The
calcium ion and amino-acid side chains in the pH 9.5 structure
are represented by a yellow sphere and red sticks, respectively.
The conformations of those amino-acid side chains are changed by
attachment of the calcium ion.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2001,
57,
1786-1792)
copyright 2001.
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Figures were
selected
by an automated process.
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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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C.Haupt,
M.Bereza,
S.T.Kumar,
B.Kieninger,
I.Morgado,
P.Hortschansky,
G.Fritz,
C.Röcken,
U.Horn,
and
M.Fändrich
(2011).
Pattern recognition with a fibril-specific antibody fragment reveals the surface variability of natural amyloid fibrils.
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J Mol Biol,
408,
529-540.
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M.Fauvart,
N.Verstraeten,
B.Dombrecht,
R.Venmans,
S.Beullens,
C.Heusdens,
and
J.Michiels
(2009).
Rhizobium etli HrpW is a pectin-degrading enzyme and differs from phytopathogenic homologues in enzymically crucial tryptophan and glycine residues.
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Microbiology,
155,
3045-3054.
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C.Creze,
S.Castang,
E.Derivery,
R.Haser,
N.Hugouvieux-Cotte-Pattat,
V.E.Shevchik,
and
P.Gouet
(2008).
The crystal structure of pectate lyase peli from soft rot pathogen Erwinia chrysanthemi in complex with its substrate.
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J Biol Chem,
283,
18260-18268.
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PDB codes:
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A.Ochiai,
T.Itoh,
Y.Maruyama,
A.Kawamata,
B.Mikami,
W.Hashimoto,
and
K.Murata
(2007).
A novel structural fold in polysaccharide lyases: Bacillus subtilis family 11 rhamnogalacturonan lyase YesW with an eight-bladed beta-propeller.
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J Biol Chem,
282,
37134-37145.
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PDB codes:
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E.W.Czerwinski,
T.Midoro-Horiuti,
M.A.White,
E.G.Brooks,
and
R.M.Goldblum
(2005).
Crystal structure of Jun a 1, the major cedar pollen allergen from Juniperus ashei, reveals a parallel beta-helical core.
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J Biol Chem,
280,
3740-3746.
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PDB code:
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W.Hashimoto,
K.Momma,
Y.Maruyama,
M.Yamasaki,
B.Mikami,
and
K.Murata
(2005).
Structure and function of bacterial super-biosystem responsible for import and depolymerization of macromolecules.
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Biosci Biotechnol Biochem,
69,
673-692.
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G.Michel,
K.Pojasek,
Y.Li,
T.Sulea,
R.J.Linhardt,
R.Raman,
V.Prabhakar,
R.Sasisekharan,
and
M.Cygler
(2004).
The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery.
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J Biol Chem,
279,
32882-32896.
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PDB codes:
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J.Jenkins,
V.E.Shevchik,
N.Hugouvieux-Cotte-Pattat,
and
R.W.Pickersgill
(2004).
The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi.
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J Biol Chem,
279,
9139-9145.
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PDB code:
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M.Yamasaki,
S.Moriwaki,
O.Miyake,
W.Hashimoto,
K.Murata,
and
B.Mikami
(2004).
Structure and function of a hypothetical Pseudomonas aeruginosa protein PA1167 classified into family PL-7: a novel alginate lyase with a beta-sandwich fold.
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J Biol Chem,
279,
31863-31872.
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PDB code:
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T.Itoh,
S.Akao,
W.Hashimoto,
B.Mikami,
and
K.Murata
(2004).
Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from Bacillus sp. GL1 at 1.8 A resolution.
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J Biol Chem,
279,
31804-31812.
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PDB code:
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A.M.Larsson,
R.Andersson,
J.Ståhlberg,
L.Kenne,
and
T.A.Jones
(2003).
Dextranase from Penicillium minioluteum: reaction course, crystal structure, and product complex.
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Structure,
11,
1111-1121.
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PDB codes:
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S.R.Herron,
R.D.Scavetta,
M.Garrett,
M.Legner,
and
F.Jurnak
(2003).
Characterization and implications of Ca2+ binding to pectate lyase C.
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J Biol Chem,
278,
12271-12277.
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PDB codes:
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W.Hashimoto,
H.Nankai,
B.Mikami,
and
K.Murata
(2003).
Crystal structure of Bacillus sp. GL1 xanthan lyase, which acts on the side chains of xanthan.
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J Biol Chem,
278,
7663-7673.
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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
codes are
shown on the right.
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Links
