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PDBsum entry 1pam
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Glycosyltransferase
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PDB id
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1pam
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Contents |
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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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X-Ray structure of cyclodextrin glucanotransferase from alkalophilic bacillus sp. 1011. Comparison of two independent molecules at 1.8 a resolution.
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Authors
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K.Harata,
K.Haga,
A.Nakamura,
M.Aoyagi,
K.Yamane.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1996,
52,
1136-1145.
[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 were identified by an automated
search of PubMed on title and author
names, giving a
perfect match.
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Abstract
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Cyclodextrin glucanotransferase (CGTase) is an enzyme which produces
cyclodextrins by the degradation of starch. The enzyme from alkalophilic
Bacillus sp. 1011, consisting of 686 amino acid residues, was crystallized from
the solution containing 20% PEG 3000 and 20% 2-propanol at pH 5.6 adjusted with
citrate buffer. The space group was P1 and the unit cell contained two molecules
(V(m) = 2.41 A(3) Da(-1)). The structure was solved by the molecular replacement
method and refined to a conventional R value of 0.161 (R(free) = 0.211) for the
reflections in the resolution range 1.8-10 A by energy minimization combined
with simulated annealing. The molecule consists of five domains, designated A-E,
and its backbone structure is similar to the structure of other bacterial
CGTases. The molecule has two calcium binding sites where calcium ions are
coordinated by seven ligands, forming a distorted pentagonal bipyramid. The two
independent molecules are related by a pseudotwofold symmetry and are
superimposed with an r.m.s. deviation value of 0.32 A for equivalent C(alpha)
atoms. Comparison of these molecules indicated the relatively large mobility of
domains C and E with respect to domain A. The active site is filled with water
molecules forming a hydrogen-bond network with polar side-chain groups. Two
water molecules commonly found in the active center of both molecules link to
several catalytically important residues by hydrogen bonds and participate in
maintaining a similar orientation of side chains in the two independent
molecules.
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Figure 4.
Fig. 4. The backbone structure of
CGTase drwn using the program
(Kraulis, 1991). The
five domains are shown with
colrs, blu (domain A), yellow
(domain B), green (domain C), red
(domain D) and light blue (domain
E). Calcim ions are denoted by
pinkcolored circles.
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Figure 5.
Fig. 5. Suprposition of the backbone structure of CGTase from B. spp. 1011 (wite), B. stearothermophilus (red), B. circulans strain 8 (bue)
and B. circulans strain 251 (green).
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Figure 13.
Fig. 13. Schematic dra\ving of the geometry of active center. Inter
atomic distances in molecule (2) are given in parenthe~,es.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(1996,
52,
1136-1145)
copyright 1996.
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