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PDBsum entry 1vav
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* Residue conservation analysis
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DOI no:
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J Biol Chem
279:31863-31872
(2004)
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PubMed id:
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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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M.Yamasaki,
S.Moriwaki,
O.Miyake,
W.Hashimoto,
K.Murata,
B.Mikami.
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ABSTRACT
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Structural and functional analyses of alginate lyases are important in the
clarification of the biofilm-dependent ecosystem in Pseudomonas aeruginosa and
in the development of therapeutic agents for bacterial disease. Most alginate
lyases are classified into polysaccharide lyase (PL) family-5 and -7 based on
their primary structures. Family PL-7 enzymes are still poorly characterized
especially in structural properties. Among family PL-7, a gene coding for a
hypothetical protein (PA1167) homologous to Sphingomonas alginate lyase A1-II
was found to be present in the P. aeruginosa genome. PA1167 overexpressed in
Escherichia coli cleaved glycosidic bonds in alginate and released unsaturated
saccharides, indicating that PA1167 is an alginate lyase catalyzing a
beta-elimination reaction. The enzyme acted preferably on heteropolymeric
regions endolytically and worked most efficiently at pH 8.5 and 40 degrees C.
The specific activity of PA1167, however, was much weaker than that of the known
alginate lyase AlgL, suggesting that AlgL plays a main role in alginate
depolymerization in P. aeruginosa. In addition to this specific activity,
differences were found between PA1167 and AlgL in enzyme properties such as
molecular mass, optimum pH, salt effect, and substrate specificity. The first
crystal structure of the family PL-7 alginate lyase was determined at 2.0 A
resolution. PA1167 was found to form a glove-like beta-sandwich composed of 15
beta-strands and 3 alpha-helices. The structural difference between the
beta-sandwich PA1167 of family PL-7 and alpha/alpha-barrel AlgL of family PL-5
may be responsible for the enzyme characteristics. Crystal structures of
polysaccharide lyases determined so far indicate that they can be assigned to
three folding groups having parallel beta-helix, alpha/alpha-barrel, and
alpha/alpha-barrel + antiparallel beta-sheet structures as basic frames. PA1167
is the fourth novel folding structure found among polysaccharide lyases.
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Selected figure(s)
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Figure 1.
FIG. 1. Block sites of alginate polymer and alginate lyase
reactions. A, MM; B, GG; C, MG block sites. M and G represent
 -D-mannuronate and  -L-guluronate. Vertical
arrows indicate cleavage sites for alginate lyase reactions and
horizontal arrows indicate those for reactions. D, reaction
scheme for the TBA method.
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Figure 5.
FIG. 5. Crystal structure of PA1167. A, overall structure
of PA1167 (stereo diagram). B, topology diagram. -Sheets
in A are shown in yellow and B in orange.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2004,
279,
31863-31872)
copyright 2004.
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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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K.Uchimura,
M.Miyazaki,
Y.Nogi,
T.Kobayashi,
and
K.Horikoshi
(2010).
Cloning and sequencing of alginate lyase genes from deep-sea strains of Vibrio and Agarivorans and characterization of a new Vibrio enzyme.
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Mar Biotechnol (NY),
12,
526-533.
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M.L.Garron,
and
M.Cygler
(2010).
Structural and mechanistic classification of uronic acid-containing polysaccharide lyases.
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Glycobiology,
20,
1547-1573.
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M.Gimmestad,
H.Ertesvåg,
T.M.Heggeset,
O.Aarstad,
B.I.Svanem,
and
S.Valla
(2009).
Characterization of three new Azotobacter vinelandii alginate lyases, one of which is involved in cyst germination.
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J Bacteriol,
191,
4845-4853.
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N.Konno,
K.Igarashi,
N.Habu,
M.Samejima,
and
A.Isogai
(2009).
Cloning of the Trichoderma reesei cDNA encoding a glucuronan lyase belonging to a novel polysaccharide lyase family.
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Appl Environ Microbiol,
75,
101-107.
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T.Kobayashi,
K.Uchimura,
M.Miyazaki,
Y.Nogi,
and
K.Horikoshi
(2009).
A new high-alkaline alginate lyase from a deep-sea bacterium Agarivorans sp.
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Extremophiles,
13,
121-129.
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K.Murata,
S.Kawai,
B.Mikami,
and
W.Hashimoto
(2008).
Superchannel of bacteria: biological significance and new horizons.
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Biosci Biotechnol Biochem,
72,
265-277.
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A.K.Arakaki,
W.Tian,
and
J.Skolnick
(2006).
High precision multi-genome scale reannotation of enzyme function by EFICAz.
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BMC Genomics,
7,
315.
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A.Ochiai,
M.Yamasaki,
B.Mikami,
W.Hashimoto,
and
K.Murata
(2006).
Crystallization and preliminary X-ray analysis of an exotype alginate lyase Atu3025 from Agrobacterium tumefaciens strain C58, a member of polysaccharide lyase family 15.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
62,
486-488.
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H.J.Jeong,
S.A.Lee,
P.D.Moon,
H.J.Na,
R.K.Park,
J.Y.Um,
H.M.Kim,
and
S.H.Hong
(2006).
Alginic acid has anti-anaphylactic effects and inhibits inflammatory cytokine expression via suppression of nuclear factor-kappaB activation.
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Clin Exp Allergy,
36,
785-794.
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J.Vasur,
R.Kawai,
A.M.Larsson,
K.Igarashi,
M.Sandgren,
M.Samejima,
and
J.Ståhlberg
(2006).
X-ray crystallographic native sulfur SAD structure determination of laminarinase Lam16A from Phanerochaete chrysosporium.
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Acta Crystallogr D Biol Crystallogr,
62,
1422-1429.
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PDB code:
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R.I.Sadreyev,
and
N.V.Grishin
(2006).
Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds.
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BMC Struct Biol,
6,
6.
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M.Yamasaki,
K.Ogura,
S.Moriwaki,
W.Hashimoto,
K.Murata,
and
B.Mikami
(2005).
Crystallization and preliminary X-ray analysis of alginate lyases A1-II and A1-II' from Sphingomonas sp. A1.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
61,
288-290.
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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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W.Hashimoto,
M.Yamasaki,
T.Itoh,
K.Momma,
B.Mikami,
and
K.Murata
(2004).
Super-channel in bacteria: structural and functional aspects of a novel biosystem for the import and depolymerization of macromolecules.
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J Biosci Bioeng,
98,
399-413.
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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
code is
shown on the right.
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Links
