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PDBsum entry 1d3c
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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The cyclization mechanism of cyclodextrin glycosyltransferase (cgtase) as revealed by a gamma-Cyclodextrin-Cgtase complex at 1.8-A resolution.
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Authors
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J.C.Uitdehaag,
K.H.Kalk,
B.A.Van der veen,
L.Dijkhuizen,
B.W.Dijkstra.
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Ref.
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J Biol Chem, 1999,
274,
34868-34876.
[DOI no: ]
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PubMed id
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Abstract
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The enzyme cyclodextrin glycosyltransferase is closely related to alpha-amylases
but has the unique ability to produce cyclodextrins (circular
alpha(1-->4)-linked glucoses) from starch. To characterize this specificity we
determined a 1.8-A structure of an E257Q/D229N mutant cyclodextrin
glycosyltransferase in complex with its product gamma-cyclodextrin, which
reveals for the first time how cyclodextrin is competently bound. Across
subsites -2, -1, and +1, the cyclodextrin ring binds in a twisted mode similar
to linear sugars, giving rise to deformation of its circular symmetry. At
subsites -3 and +2, the cyclodextrin binds in a manner different from linear
sugars. Sequence comparisons and site-directed mutagenesis experiments support
the conclusion that subsites -3 and +2 confer the cyclization activity in
addition to subsite -6 and Tyr-195. On this basis, a role of the individual
residues during the cyclization reaction cycle is proposed.
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Figure 3.
Fig. 3. Stereo picture indicating the maltononaose (7)
(gray) and  -cyclodextrin
(black) conformation in the CGTase active site. The white C  backbone
has the conformation observed in the -cyclodextrin
complex. The backbone conformations of the loops 87-93 144-151,
175-182, and 190-199 in the maltononaose complex are indicated
in gray.
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Figure 5.
Fig. 5. Overview of the interactions between CGTase and
maltononaose (7) (A) or -cyclodextrin
(B). The distances associated with the interactions are in Table
III. For clarity, not all interactions at subsites  2, 1, and +1
are shown. Symm rel. contacts, contacts made to a
symmetry-related CGTase molecule in the crystal.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(1999,
274,
34868-34876)
copyright 1999.
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Secondary reference #1
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Title
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X-Ray structures along the reaction pathway of cyclodextrin glycosyltransferase elucidate catalysis in the alpha-Amylase family.
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Authors
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J.C.Uitdehaag,
R.Mosi,
K.H.Kalk,
B.A.Van der veen,
L.Dijkhuizen,
S.G.Withers,
B.W.Dijkstra.
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Ref.
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Nat Struct Biol, 1999,
6,
432-436.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Scheme of the CGTase reaction mechanism. The first
step, leading to intermediate formation, is explained in the
text. In the second step, Glu 257 activates an acceptor that
subsequently reacts with the intermediate, leading to product
formation. This proceeds with a mechanism that is essentially
the reverse of the first step. The glucoside ring atom
nomenclature is incorporated in the left-most picture. The
shaded orbital represents the electrons that are in a proper
orientation to participate in the cleavage of the substrate  -glycosidic
bond according to the stereo-electronic theory^22. However, when
the intermediate  -glycosyl-enzyme
bond is cleaved, such a correctly oriented orbital is not
present, as pointed out in the text.
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Figure 2.
Figure 2. Stereoview of the substrate bound to CGTase. The
maltononaose binds from subsites -7 to +2, but for clarity only
subsites -2, -1 and +1 are shown. The arrow indicates the
scissile bond. a, Showing how the substrate fits into the 2F[o]
- F[c] electron density (1  contoured),
which was calculated with F[c] and phases from unliganded CGTase
to avoid bias^16. b, The substrate distortion at the catalytic
subsite -1 (central sugar ring) is revealed by superposition
with the minimum energy conformation of maltose (orange)^15. The
superposition is based on the glucose C3, C4 and C5 atoms in
subsite -1. Comparing the substrate ring puckering parameters
with a potential map from molecular mechanics calculations
indicates that the glucose ring at the catalytic subsite is
strained by ~17 kJ mol^−1 and has a ^4C[1] chair conformation
distorted towards a ^2H[3] half chair^15. c, Undistorted (free)
maltose clearly does not fit the 2F[o] - F[c] electron density
at subsite -1. The glycosidic bond torsion angles of maltose
were adjusted to fit the density at subsite +1.
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The above figures are
reproduced from the cited reference
with permission from Macmillan Publishers Ltd
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Secondary reference #2
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Title
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Crystallographic studies of the interaction of cyclodextrin glycosyltransferase from bacillus circulans strain 251 with natural substrates and products.
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Authors
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R.M.Knegtel,
B.Strokopytov,
D.Penninga,
O.G.Faber,
H.J.Rozeboom,
K.H.Kalk,
L.Dijkhuizen,
B.W.Dijkstra.
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Ref.
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J Biol Chem, 1995,
270,
29256-29264.
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PubMed id
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Secondary reference #3
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Title
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Structure of cyclodextrin glycosyltransferase complexed with a maltononaose inhibitor at 2.6 angstrom resolution. Implications for product specificity.
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Authors
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B.Strokopytov,
R.M.Knegtel,
D.Penninga,
H.J.Rozeboom,
K.H.Kalk,
L.Dijkhuizen,
B.W.Dijkstra.
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Ref.
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Biochemistry, 1996,
35,
4241-4249.
[DOI no: ]
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PubMed id
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