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PDBsum entry 3a23
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References listed in PDB file
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Key reference
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Title
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A beta-L-Arabinopyranosidase from streptomyces avermitilis is a novel member of glycoside hydrolase family 27.
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Authors
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H.Ichinose,
Z.Fujimoto,
M.Honda,
K.Harazono,
Y.Nishimoto,
A.Uzura,
S.Kaneko.
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Ref.
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J Biol Chem, 2009,
284,
25097-25106.
[DOI no: ]
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PubMed id
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Note: In the PDB file this reference is
annotated as "TO BE PUBLISHED". The citation details given above have
been manually determined.
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Abstract
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Arabinogalactan proteins (AGPs) are a family of plant cell surface proteoglycans
and are considered to be involved in plant growth and development. Because AGPs
are very complex molecules, glycoside hydrolases capable of degrading AGPs are
powerful tools for analyses of the AGPs. We previously reported such enzymes
from Streptomyces avermitilis. Recently, a beta-l-arabinopyranosidase was
purified from the culture supernatant of the bacterium, and its corresponding
gene was identified. The primary structure of the protein revealed that the
catalytic module was highly similar to that of glycoside hydrolase family 27
(GH27) alpha-d-galactosidases. The recombinant protein was successfully
expressed as a secreted 64-kDa protein using a Streptomyces expression system.
The specific activity toward p-nitrophenyl-beta-l-arabinopyranoside was 18
micromol of arabinose/min/mg, which was 67 times higher than that toward p-
nitrophenyl-alpha-d-galactopyranoside. The enzyme could remove 0.1 and 45%
l-arabinose from gum arabic or larch arabinogalactan, respectively. X-ray
crystallographic analysis reveals that the protein had a GH27 catalytic domain,
an antiparallel beta-domain containing Greek key motifs, another antiparallel
beta-domain forming a jellyroll structure, and a carbohydrate-binding module
family 13 domain. Comparison of the structure of this protein with that of
alpha-d-galactosidase showed a single amino acid substitution (aspartic acid to
glutamic acid) in the catalytic pocket of beta-l-arabinopyranosidase, and a
space for the hydroxymethyl group on the C-5 carbon of d-galactose bound to
alpha-galactosidase was changed in beta-l-arabinopyranosidase. Mutagenesis study
revealed that the residue is critical for modulating the enzyme activity. This
is the first report in which beta-l-arabinopyranosidase is classified as a new
member of the GH27 family.
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Figure 3.
The F[obs] − F[calc] electron density maps contoured at 3
σ for the l-arabinose (A) and galactose (B) molecules bound in
the catalytic pocket in the sugar complex structures. Carbon
atoms are numbered.
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Figure 4.
A, structure of the catalytic pocket of SaArap27A in the
l-arabinose complex structure. Hydrogen bonds between SaArap27A
and bound l-arabinose (Arap) and glycerol (Gal) are shown as a
dashed cyan line. B, structure of the catalytic pocket of
SaArap27A in the galactose complex. C, superimposition of the
catalytic pocket between SaArap27A (blue) and rice
α-galactosidase (brown, PDB entry 1UAS). D, structure of the l-
arabinose-binding pocket in the subdomain α of SaArap27A domain
IV in the l-arabinose complex structure. Hydrogen bonds between
SaArap27A and the bound l-arabinose are shown as a dashed cyan
line. E and F, l-arabinose binding pocket in subdomains β and
γ of SaArap27A domain IV in the l-arabinose complex structure.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2009,
284,
25097-25106)
copyright 2009.
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Secondary reference #1
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Title
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Crystallization and preliminary crystallographic analysis of exo-Alpha-1,5-L-Arabinofuranosidase from streptomyces avermitilis nbrc14893.
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Authors
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Z.Fujimoto,
H.Ichinose,
S.Kaneko.
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Ref.
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Acta Crystallogr Sect F Struct Biol Cryst Commun, 2008,
64,
1007-1009.
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PubMed id
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