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Contents |
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* Residue conservation analysis
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PDB id:
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Hydrolase
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Title:
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1,3-alpha-1,4-beta-d-galactose-4-sulfate- 3,6-anhydro-d-galactose-2-sulfate 4 galactohydrolase
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Structure:
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Iota-carrageenase. Chain: a, b. Fragment: catalytic domain residues 28-491. Engineered: yes. Other_details: complexed with calcium, sodium and chloride
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Source:
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Alteromonas sp. Atcc43554. Organism_taxid: 116059. Strain: b834(de3). Plasmid: pet20b. Gene: cgia. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: his-tag, selemethionyl protein.
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Resolution:
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1.6Å
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R-factor:
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0.207
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R-free:
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0.223
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Authors:
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G.Michel,L.Chantalat,O.Dideberg
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Key ref:
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G.Michel
et al.
(2001).
The iota-carrageenase of Alteromonas fortis. A beta-helix fold-containing enzyme for the degradation of a highly polyanionic polysaccharide.
J Biol Chem,
276,
40202-40209.
PubMed id:
Ref:
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Date:
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22-Jan-01
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Release date:
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27-Nov-01
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PROCHECK
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Headers
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References
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Q9F5I8
(CGIA_ALTFO) -
Iota-carrageenase
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Seq:
Struc:
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491 a.a.
433 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Gene Ontology (GO) functional annotation
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Cellular component
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extracellular region
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2 terms
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Biological process
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metabolic process
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4 terms
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Biochemical function
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hydrolase activity
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2 terms
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J Biol Chem
276:40202-40209
(2001)
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PubMed id:
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The iota-carrageenase of Alteromonas fortis. A beta-helix fold-containing enzyme for the degradation of a highly polyanionic polysaccharide.
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G.Michel,
L.Chantalat,
E.Fanchon,
B.Henrissat,
B.Kloareg,
O.Dideberg.
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ABSTRACT
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Carrageenans are gel-forming hydrocolloids extracted from the cell walls of
marine red algae. They consist of d-galactose residues bound by alternate
alpha(1-->3) and beta(1-->4) linkages and substituted by one
(kappa-carrageenan), two (iota-carrageenan), or three (lambda-carrageenan)
sulfate-ester groups per disaccharide repeating unit. Both the kappa- and
iota-carrageenan chains adopt ordered conformations leading to the formation of
highly ordered aggregates of double-stranded helices. Several
kappa-carrageenases and iota-carrageenases have been cloned from marine
bacteria. Kappa-carrageenases belong to family 16 of the glycoside hydrolases,
which essentially encompasses polysaccharidases specialized in the hydrolysis of
the neutral polysaccharides such as agarose, laminarin, lichenan, and
xyloglucan. In contrast, iota-carrageenases constitute a novel glycoside
hydrolase structural family. We report here the crystal structure of Alteromonas
fortis iota-carrageenase at 1.6 A resolution. The enzyme folds into a
right-handed parallel beta-helix of 10 complete turns with two additional
C-terminal domains. Glu(245), Asp(247), or Glu(310), in the cleft of the enzyme,
are proposed as candidate catalytic residues. The protein contains one sodium
and one chloride binding site and three calcium binding sites shown to be
involved in stabilizing the enzyme structure.
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Selected figure(s)
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Figure 2.
Fig. 2. Solvent-flattened multiple anomalous diffraction
electron density map at 1.6 Å resolution. Map contoured at
2.0  of the
N-terminal calcium-binding hairpin loop. Calcium ion and water
molecules are indicated as yellow and red spheres, respectively.
The oxygen, nitrogen, and carbon atoms in the protein are shown
in red, blue, and yellow, respectively. This figure was created
using O (23).
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Figure 6.
Fig. 6.  -Carrageenan
recognition by -carrageenase.
A, view of the molecular surface of the -carrageenase
groove. The potential catalytic residues and the conserved basic
amino acids are shown in red and blue, respectively. The
distances between clusters of basic residues are shown. Fig. 6
was created using Grasp (51). B, ball and stick representation
of a -neocarrahexaose-sulfate
(7). Oxygen, sulfur, and carbon atoms are shown in red, yellow,
and black, respectively. Distances between the sulfate
substituents are shown.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2001,
276,
40202-40209)
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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G.Michel,
P.Nyval-Collen,
T.Barbeyron,
M.Czjzek,
and
W.Helbert
(2006).
Bioconversion of red seaweed galactans: a focus on bacterial agarases and carrageenases.
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Appl Microbiol Biotechnol, 71,
23-33.
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S.A.Douthit,
M.Dlakic,
D.E.Ohman,
and
M.J.Franklin
(2005).
Epimerase active domain of Pseudomonas aeruginosa AlgG, a protein that contains a right-handed beta-helix.
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J Bacteriol, 187,
4573-4583.
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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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A.Vasella,
G.J.Davies,
and
M.Böhm
(2002).
Glycosidase mechanisms.
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Curr Opin Chem Biol, 6,
619-629.
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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
