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PDBsum entry 2b5d
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References listed in PDB file
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Key reference
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Title
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Structure of the novel alpha-Amylase amyc from thermotoga maritima.
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Authors
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A.Dickmanns,
M.Ballschmiter,
W.Liebl,
R.Ficner.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2006,
62,
262-270.
[DOI no: ]
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PubMed id
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Abstract
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alpha-Amylases are essential enzymes in alpha-glucan metabolism and catalyse the
hydrolysis of long sugar polymers such as amylose and starch. The crystal
structure of a previously unidentified amylase (AmyC) from the hyperthermophilic
organism Thermotoga maritima was determined at 2.2 A resolution by means of MAD.
AmyC lacks sequence similarity to canonical alpha-amylases, which belong to
glycosyl hydrolase families 13, 70 and 77, but exhibits significant similarity
to a group of as yet uncharacterized proteins in COG1543 and is related to
glycerol hydrolase family 57 (GH-57). AmyC reveals features that are
characteristic of alpha-amylases, such as a distorted TIM-barrel structure
formed by seven beta-strands and alpha-helices (domain A), and two additional
but less well conserved domains. The latter are domain B, which contains three
helices inserted in the TIM-barrel after beta-sheet 2, and domain C, a
five-helix region at the C-terminus. Interestingly, despite moderate sequence
homology, structure comparison revealed significant similarities to a member of
GH-57 with known three-dimensional structure, Thermococcus litoralis
4-glucanotransferase, and an even higher similarity to a structure of an enzyme
of unknown function from Thermus thermophilus.
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Figure 1.
Figure 1 AmyC shows the characteristics of a functional amylase.
(a) A Lineweaver-Burk diagram showing the kinetics of the
hydrolysis of starch by AmyC allows the calculation of a K[m]
value of 1.1 mg ml-1 and a V[max] of 1.3 U mg-1. (b) AmyC
activity is inhibited by the classical amylase inhibitor
acarbose. The activity of Amy C is reduced to 25 or 20% using a
31-fold or 77-fold excess of acarbose, respectively.
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The above figure is
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2006,
62,
262-270)
copyright 2006.
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