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PDBsum entry 2b5d
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* Residue conservation analysis
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Enzyme class:
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E.C.3.2.1.1
- alpha-amylase.
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Reaction:
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Endohydrolysis of 1,4-alpha-glucosidic linkages in oligosaccharides and polysaccharides.
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DOI no:
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Acta Crystallogr D Biol Crystallogr
62:262-270
(2006)
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PubMed id:
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Structure of the novel alpha-amylase AmyC from Thermotoga maritima.
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A.Dickmanns,
M.Ballschmiter,
W.Liebl,
R.Ficner.
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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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Selected figure(s)
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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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Figure was
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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C.R.Santos,
C.C.Tonoli,
D.M.Trindade,
C.Betzel,
H.Takata,
T.Kuriki,
T.Kanai,
T.Imanaka,
R.K.Arni,
and
M.T.Murakami
(2011).
Structural basis for branching-enzyme activity of glycoside hydrolase family 57: structure and stability studies of a novel branching enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1.
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Proteins,
79,
547-557.
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PDB codes:
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S.B.Conners,
E.F.Mongodin,
M.R.Johnson,
C.I.Montero,
K.E.Nelson,
and
R.M.Kelly
(2006).
Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species.
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FEMS Microbiol Rev,
30,
872-905.
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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
codes are
shown on the right.
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Links
