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PDBsum entry 1h7h
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Nucleotidyltransferase
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PDB id
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1h7h
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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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The structure of cmp:2-Keto-3-Deoxy-Manno-Octonic acid synthetase and of its complexes with substrates and substrate analogs.
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Authors
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S.Jelakovic,
G.E.Schulz.
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Ref.
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J Mol Biol, 2001,
312,
143-155.
[DOI no: ]
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PubMed id
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Abstract
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The enzyme CMP-Kdo synthetase (CKS) catalyzes the activation of the sugar Kdo
(2-keto-3-deoxy-manno-octonic acid) by forming a monophosphate diester. CKS is a
pharmaceutical target because CMP-Kdo is used in the biosynthesis of
lipopolysaccharides that are vital for Gram-negative bacteria. We have refined
the structure of the unligated capsule-specific CKS from Escherichia coli at 1.8
A resolution (1 A=0.1 nm) and we have established the structures of its
complexes with the substrate CTP, with CDP and CMP as well as with the product
analog CMP-NeuAc (CMP-sialate) by X-ray diffraction analyses at resolutions
between 2.1 A and 2.5 A. The N-terminal domains of the dimeric enzyme bind CTP
in a peculiar nucleotide-binding fold, whereas the C-terminal domains form the
dimer interface. The observed binding geometries together with the amino acid
variabilities during evolution and the locations of a putative Mg(2+) and of a
very strongly bound water molecule suggest a pathway for the catalysis. The
N-terminal domain shows sequence homology with the CMP-NeuAc synthetases.
Moreover, the chain fold and the substrate-binding position of CKS resemble
those of other enzymes processing nucleotide-sugars.
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Figure 3.
Figure 3. Stereo ribbon plot of the CKS dimer viewed along
the molecular 2-fold axis. Subunit B (blue) is at the top. In
the crystals this subunit binds the nucleotides and the analog
CMP-NeuAc (here displayed). The domains are given in different
hues. The exceptional left-handed connection between b6 and b7
is marked red, it connects the two domains. The bulge residues
of b10 are marked by balls.
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Figure 9.
Figure 9. Proposed reaction mechanism of CKS. The b- and
g-phosphates of CTP are bound in the so-called PP-loop. Kdo is
displayed at the position of the NeuAc moiety of bound CMP-NeuAc
without trying to state a contact to a surrounding residue.
During the nucleophilic attack Arg10 moves from the b-phosphate
away to Asp51, and Lys19 moves from the b- to the a-phosphate. A
strongly bound water molecule between the carboxylates of Asp98
and Asp225 is considered to be the base accepting the hydroxyl
proton.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2001,
312,
143-155)
copyright 2001.
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Secondary reference #1
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Title
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The three-Dimensional structure of capsule-Specific cmp: 2-Keto-3-Deoxy-Manno-Octonic acid synthetase from escherichia coli.
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Authors
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S.Jelakovic,
K.Jann,
G.E.Schulz.
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Ref.
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FEBS Lett, 1996,
391,
157-161.
[DOI no: ]
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PubMed id
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