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PDBsum entry 1b5d
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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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Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage t4, A component of the deoxyribonucleoside triphosphate-Synthesizing complex.
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Authors
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H.K.Song,
S.H.Sohn,
S.W.Suh.
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Ref.
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EMBO J, 1999,
18,
1104-1113.
[DOI no: ]
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PubMed id
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Abstract
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Bacteriophage T4 deoxycytidylate hydroxymethylase (EC 2.1.2.8), a homodimer of
246-residue subunits, catalyzes hydroxymethylation of the cytosine base in
deoxycytidylate (dCMP) to produce 5-hydroxymethyl-dCMP. It forms part of a phage
DNA protection system and appears to function in vivo as a component of a
multienzyme complex called deoxyribonucleoside triphosphate (dNTP) synthetase.
We have determined its crystal structure in the presence of the substrate dCMP
at 1.6 A resolution. The structure reveals a subunit fold and a dimerization
pattern in common with thymidylate synthases, despite low (approximately 20%)
sequence identity. Among the residues that form the dCMP binding site, those
interacting with the sugar and phosphate are arranged in a configuration similar
to the deoxyuridylate binding site of thymidylate synthases. However, the
residues interacting directly or indirectly with the cytosine base show a more
divergent structure and the presumed folate cofactor binding site is more open.
Our structure reveals a water molecule properly positioned near C-6 of cytosine
to add to the C-7 methylene intermediate during the last step of
hydroxymethylation. On the basis of sequence comparison and crystal packing
analysis, a hypothetical model for the interaction between T4 deoxycytidylate
hydroxymethylase and T4 thymidylate synthase in the dNTP-synthesizing complex
has been built.
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Figure 4.
Figure 4 Ribbon diagram comparing the subunit folds of T4 CH
(left) and E.coli TS (right). The structurally similar parts are
colored in blue and the remaining parts in orange. The
catalytically important residues (Glu60, Cys148 and Asp179 in T4
CH; Glu58, Cys146 and Asn177 in E.coli TS) are shown in green.
The substrates dCMP in T4 CH and dUMP in E.coli TS are drawn in
deep blue and the cofactor analog CB3717 bound to E.coli TS is
in magenta. This figure was drawn by MOLSCRIPT (Kraulis, 1991)
and RASTER 3D (Merritt and Murphy, 1994).
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Figure 5.
Figure 5 Schematic diagram of the hydrogen-bond network in the
active site of T4 CH. The distance between the S  atom
of Cys148 and the guanidium group of Arg168 (3.3 Å) is
indicated.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(1999,
18,
1104-1113)
copyright 1999.
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