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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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Structure of the thermostable arabinanase
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Structure:
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Arabinanase-ts. Chain: a. Synonym: endo-1,5-alpha-l-arabinanase, arabinase-ts, rabinan endo-1,5-alpha-l-arabinosidase. Engineered: yes
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Source:
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Geobacillus thermodenitrificans. Organism_taxid: 33940. Strain: ts-3. Expressed in: bacillus subtilis. Expression_system_taxid: 1423.
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Resolution:
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1.90Å
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R-factor:
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0.183
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R-free:
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0.225
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Authors:
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A.Yamaguchi,T.Tada,T.Nakaniwa,T.Kitatani
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Key ref:
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A.Yamaguchi
et al.
(2005).
Structural basis for thermostability of endo-1,5-alpha-L-arabinanase from Bacillus thermodenitrificans TS-3.
J Biochem (tokyo),
137,
587-592.
PubMed id:
DOI:
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Date:
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21-Jun-04
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Release date:
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21-Jun-05
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PROCHECK
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Headers
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References
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Q93HT9
(Q93HT9_9BACI) -
Arabinase-TS
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Seq:
Struc:
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313 a.a.
312 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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Biological process
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carbohydrate metabolic process
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1 term
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Biochemical function
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hydrolase activity, hydrolyzing O-glycosyl compounds
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1 term
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DOI no:
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J Biochem (tokyo)
137:587-592
(2005)
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PubMed id:
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Structural basis for thermostability of endo-1,5-alpha-L-arabinanase from Bacillus thermodenitrificans TS-3.
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A.Yamaguchi,
T.Tada,
K.Wada,
T.Nakaniwa,
T.Kitatani,
Y.Sogabe,
M.Takao,
T.Sakai,
K.Nishimura.
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ABSTRACT
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The crystal structure of a thermostable endo-1,5-alpha-L-arabinanase, ABN-TS,
from Bacillus thermodenitrificans TS-3 was determined at 1.9 A to an R-factor of
18.3% and an R-free-factor of 22.5%. The enzyme molecule has a five-bladed
beta-propeller fold. The substrate-binding cleft formed across one face of the
propeller is open on both sides to allow random binding of several sugar units
in the polymeric substrate arabinan. The beta-propeller fold is stabilized
through a ring closure. ABN-TS exhibits a new closure-mode involving residues in
the N-terminal region: Phe7 to Gly21 exhibit hydrogen bonds and hydrophobic
interactions with the first and last blades, and Phe4 links the second and third
blades through a hydrogen bond and an aromatic stacking interaction,
respectively. The role of the N-terminal region in the thermostability was
confirmed with a mutant lacking 16 amino acid residues from the N-terminus of
ABN-TS.
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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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Y.Sogabe,
T.Kitatani,
A.Yamaguchi,
T.Kinoshita,
H.Adachi,
K.Takano,
T.Inoue,
Y.Mori,
H.Matsumura,
T.Sakamoto,
and
T.Tada
(2011).
High-resolution structure of exo-arabinanase from Penicillium chrysogenum.
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Acta Crystallogr D Biol Crystallogr, 67,
415-422.
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PDB codes:
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A.Bhardwaj,
S.Leelavathi,
S.Mazumdar-Leighton,
A.Ghosh,
S.Ramakumar,
and
V.S.Reddy
(2010).
The critical role of N- and C-terminal contact in protein stability and folding of a family 10 xylanase under extreme conditions.
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PLoS One, 5,
e11347.
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D.de Sanctis,
J.M.Inácio,
P.F.Lindley,
I.de Sá-Nogueira,
and
I.Bento
(2010).
New evidence for the role of calcium in the glycosidase reaction of GH43 arabinanases.
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FEBS J, 277,
4562-4574.
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PDB codes:
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A.Alhassid,
A.Ben-David,
O.Tabachnikov,
D.Libster,
E.Naveh,
G.Zolotnitsky,
Y.Shoham,
and
G.Shoham
(2009).
Crystal structure of an inverting GH 43 1,5-alpha-L-arabinanase from Geobacillus stearothermophilus complexed with its substrate.
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Biochem J, 422,
73-82.
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PDB codes:
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R.Carapito,
A.Imberty,
J.M.Jeltsch,
S.C.Byrns,
P.H.Tam,
T.L.Lowary,
A.Varrot,
and
V.Phalip
(2009).
Molecular basis of arabinobio-hydrolase activity in phytopathogenic fungi: crystal structure and catalytic mechanism of Fusarium graminearum GH93 exo-alpha-L-arabinanase.
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J Biol Chem, 284,
12285-12296.
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PDB codes:
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W.Lammens,
K.Le Roy,
L.Schroeven,
A.Van Laere,
A.Rabijns,
and
W.Van den Ende
(2009).
Structural insights into glycoside hydrolase family 32 and 68 enzymes: functional implications.
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J Exp Bot, 60,
727-740.
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D.W.Wong,
V.J.Chan,
and
S.B.Batt
(2008).
Cloning and characterization of a novel exo-alpha-1,5-L-arabinanase gene and the enzyme.
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Appl Microbiol Biotechnol, 79,
941-949.
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D.de Sanctis,
I.Bento,
J.M.Inácio,
S.Custódio,
I.de Sá-Nogueira,
and
M.A.Carrondo
(2008).
Overproduction, crystallization and preliminary X-ray characterization of Abn2, an endo-1,5-alpha-arabinanase from Bacillus subtilis.
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Acta Crystallogr Sect F Struct Biol Cryst Commun, 64,
636-638.
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M.Verhaest,
W.Lammens,
K.Le Roy,
B.De Coninck,
C.J.De Ranter,
A.Van Laere,
W.Van den Ende,
and
A.Rabijns
(2006).
X-ray diffraction structure of a cell-wall invertase from Arabidopsis thaliana.
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Acta Crystallogr D Biol Crystallogr, 62,
1555-1563.
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PDB code:
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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
