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PDBsum entry 1v1s
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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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Structure of thermus thermophilus 2-Keto-3-Deoxygluconate kinase: evidence for recognition of an open chain substrate.
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Authors
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N.Ohshima,
E.Inagaki,
K.Yasuike,
K.Takio,
T.H.Tahirov.
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Ref.
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J Mol Biol, 2004,
340,
477-489.
[DOI no: ]
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PubMed id
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Abstract
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2-Keto-3-deoxygluconate kinase (KDGK) catalyzes the phosphorylation of
2-keto-3-deoxygluconate (KDG) to 2-keto-3-deoxy-6-phosphogluconate (KDGP). The
genome sequence of Thermus thermophilus HB8 contains an open reading frame that
has a 30% identity to Escherichia coli KDGK. The KDGK activity of T.thermophilus
protein (TtKDGK) has been confirmed, and its crystal structure has been
determined by the molecular replacement method and refined with two crystal
forms to 2.3 angstroms and 3.2 angstroms, respectively. The enzyme is a hexamer
organized as a trimer of dimers. Each subunit is composed of two domains, a
larger alpha/beta domain and a smaller beta-sheet domain, similar to that of
ribokinase and adenosine kinase, members of the PfkB family of carbohydrate
kinases. Furthermore, the TtKDGK structure with its KDG and ATP analogue was
determined and refined at 2.1 angstroms. The bound KDG was observed
predominantly as an open chain structure. The positioning of ligands and the
conservation of important catalytic residues suggest that the reaction mechanism
is likely to be similar to that of other members of the PfkB family, including
ribokinase. In particular, the Asp251 is postulated to have a role in
transferring the gamma-phosphate of ATP to the 5'-hydroxyl group of KDG.
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Figure 2.
Figure 2. The overall view of (a) TtKDGK and (b) EcRK
dimers. The view is parallel to the pseudo 2-fold axis in (a)
and crystallographic 2-fold axis in (b). Subunits are
represented by ribbons and are colored green and cyan. The bound
ligands are drawn by balls and sticks. The figure was prepared
using Molscript[30.] and Raster3D. [30.]
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Figure 5.
Figure 5. The KDG binding. (a) 2F[o] -F[c] Fourier maps of
bound KDG in the A subunit of TtKDGK. The open chain keto form
of KDG and side-chain of Arg167 colored by atom colors: carbon
atoms in yellow, nitrogen atoms in cyan and oxygen atoms in red.
The modeled a-furanose form of KDG is in cyan. (b) and (c) The
hydrogen bonds between the KDG and (b) A and (c) B subunits of
TtKDGK. (a) Was prepared using TURBO-FRODO and the (b) and (c)
were prepared using Molscript[30.] and Raster3D. [31.]
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2004,
340,
477-489)
copyright 2004.
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Secondary reference #1
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Title
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Crystallization and preliminary crystallographic analysis of 2-Keto-3-Deoxygluconate kinase from thermus thermophilus.
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Authors
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E.Inagaki,
Y.Ukita,
M.Kumei,
Y.Kajihara,
T.H.Tahirov.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2004,
60,
761-763.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1 Photomicrographs of (a) triangular and (b) hexagonal
plate-shaped crystals.
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The above figure is
reproduced from the cited reference
with permission from the IUCr
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