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PDBsum entry 2d0h
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* Residue conservation analysis
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Enzyme class:
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E.C.3.2.1.135
- neopullulanase.
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Reaction:
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Hydrolysis of pullulan to panose (6-alpha-D-glucosylmaltose).
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DOI no:
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FEBS J
272:6145-6153
(2005)
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PubMed id:
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Complexes of Thermoactinomyces vulgaris R-47 alpha-amylase 1 and pullulan model oligossacharides provide new insight into the mechanism for recognizing substrates with alpha-(1,6) glycosidic linkages.
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A.Abe,
H.Yoshida,
T.Tonozuka,
Y.Sakano,
S.Kamitori.
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ABSTRACT
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Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) has unique hydrolyzing
activities for pullulan with sequence repeats of alpha-(1,4), alpha-(1,4), and
alpha-(1,6) glycosidic linkages, as well as for starch. TVAI mainly hydrolyzes
alpha-(1,4) glycosidic linkages to produce a panose, but it also hydrolyzes
alpha-(1,6) glycosidic linkages with a lesser efficiency. X-ray structures of
three complexes comprising an inactive mutant TVAI (D356N or D356N/E396Q) and a
pullulan model oligosaccharide (P2;
[Glc-alpha-(1,6)-Glc-alpha-(1,4)-Glc-alpha-(1,4)]2 or P5;
[Glc-alpha-(1,6)-Glc-alpha-(1,4)-Glc-alpha-(1,4)]5) were determined. The complex
D356N/P2 is a mimic of the enzyme/product complex in the main catalytic reaction
of TVAI, and a structural comparison with Aspergillus oryzaealpha-amylase showed
that the (-) subsites of TVAI are responsible for recognizing both starch and
pullulan. D356N/E396Q/P2 and D356N/E396Q/P5 provided models of the
enzyme/substrate complex recognizing the alpha-(1,6) glycosidic linkage at the
hydrolyzing site. They showed that only subsites -1 and -2 at the nonreducing
end of TVAI are effective in the hydrolysis of alpha-(1,6) glycosidic linkages,
leading to weak interactions between substrates and the enzyme. Domain N of TVAI
is a starch-binding domain acting as an anchor in the catalytic reaction of the
enzyme. In this study, additional substrates were also found to bind to domain
N, suggesting that domain N also functions as a pullulan-binding domain.
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Selected figure(s)
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Figure 1.
Fig. 1. Chemical structures of the repeat units of
pullulan, P2 and P5. A solid arrow indicates the main
hydrolysing site, and a dashed arrow indicates the minor site of
pullulan hydrolysed by TVAI.
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Figure 2.
Fig. 2. Overall structure of TVAI (D356N/E396Q/P5).
Domains N, A, B, and C are drawn in blue, green, yellow, and
pink, respectively. The binding substrates and Ca^2+ are shown
by a wire-style model and as orange spheres. The catalytic site,
site-N, site-NA, site-A, and site-C, are labelled. The loop
region from Ser282 to Gln284 in D356N/E396Q/P2 with poor
electron density is shown in red.
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The above figures are
reprinted
by permission from the Federation of European Biochemical Societies:
FEBS J
(2005,
272,
6145-6153)
copyright 2005.
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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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R.Suzuki,
T.Katayama,
M.Kitaoka,
H.Kumagai,
T.Wakagi,
H.Shoun,
H.Ashida,
K.Yamamoto,
and
S.Fushinobu
(2009).
Crystallographic and mutational analyses of substrate recognition of endo-alpha-N-acetylgalactosaminidase from Bifidobacterium longum.
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J Biochem,
146,
389-398.
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PDB code:
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M.E.Caines,
H.Zhu,
M.Vuckovic,
L.M.Willis,
S.G.Withers,
W.W.Wakarchuk,
and
N.C.Strynadka
(2008).
The Structural Basis for T-antigen Hydrolysis by Streptococcus pneumoniae: A TARGET FOR STRUCTURE-BASED VACCINE DESIGN.
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J Biol Chem,
283,
31279-31283.
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PDB code:
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M.Kitamura,
M.Okuyama,
F.Tanzawa,
H.Mori,
Y.Kitago,
N.Watanabe,
A.Kimura,
I.Tanaka,
and
M.Yao
(2008).
Structural and Functional Analysis of a Glycoside Hydrolase Family 97 Enzyme from Bacteroides thetaiotaomicron.
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J Biol Chem,
283,
36328-36337.
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PDB codes:
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Y.Xu,
M.Yang,
J.Sun,
J.Qian,
D.Zhang,
Y.Sun,
L.Ma,
and
C.Zhu
(2008).
Glycogen branching enzyme: a novel deltamethrin resistance-associated gene from Culex pipiens pallens.
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Parasitol Res,
103,
449-458.
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S.Bozonnet,
M.T.Jensen,
M.M.Nielsen,
N.Aghajari,
M.H.Jensen,
B.Kramhøft,
M.Willemoës,
S.Tranier,
R.Haser,
and
B.Svensson
(2007).
The 'pair of sugar tongs' site on the non-catalytic domain C of barley alpha-amylase participates in substrate binding and activity.
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FEBS J,
274,
5055-5067.
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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
code is
shown on the right.
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Links
