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Structural genomics, unknown function
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PDB id
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1nrk
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Contents |
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* Residue conservation analysis
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Gene Ontology (GO) functional annotation
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Cellular component
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cytoplasm
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1 term
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Biological process
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RNA modification
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3 terms
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Biochemical function
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folic acid binding
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2 terms
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DOI no:
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J Bacteriol
186:7134-7140
(2004)
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PubMed id:
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Crystal structure of the YgfZ protein from Escherichia coli suggests a folate-dependent regulatory role in one-carbon metabolism.
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A.Teplyakov,
G.Obmolova,
E.Sarikaya,
S.Pullalarevu,
W.Krajewski,
A.Galkin,
A.J.Howard,
O.Herzberg,
G.L.Gilliland.
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ABSTRACT
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The ygfZ gene product of Escherichia coli represents a large protein family
conserved in bacteria to eukaryotes. The members of this family are
uncharacterized proteins with marginal sequence similarity to the T-protein
(aminomethyltransferase) of the glycine cleavage system. To assist with the
functional assignment of the YgfZ family, the crystal structure of the E. coli
protein was determined by multiwavelength anomalous diffraction. The protein
molecule has a three-domain architecture with a central hydrophobic channel. The
structure is very similar to that of bacterial dimethylglycine oxidase, an
enzyme of the glycine betaine pathway and a homolog of the T-protein. Based on
structural superposition, a folate-binding site was identified in the central
channel of YgfZ, and the ability of YgfZ to bind folate derivatives was
confirmed experimentally. However, in contrast to dimethylglycine oxidase and
T-protein, the YgfZ family lacks amino acid conservation at the folate site,
which implies that YgfZ is not an aminomethyltransferase but is likely a
folate-dependent regulatory protein involved in one-carbon metabolism.
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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.N.Lin,
W.J.Syu,
W.S.Sun,
J.W.Chen,
T.H.Chen,
M.J.Don,
and
S.H.Wang
(2010).
A role of ygfZ in the Escherichia coli response to plumbagin challenge.
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J Biomed Sci, 17,
84.
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J.C.Waller,
S.Alvarez,
V.Naponelli,
A.Lara-Nuñez,
I.K.Blaby,
V.Da Silva,
M.J.Ziemak,
T.J.Vickers,
S.M.Beverley,
A.S.Edison,
J.R.Rocca,
J.F.Gregory,
V.de Crécy-Lagard,
and
A.D.Hanson
(2010).
A role for tetrahydrofolates in the metabolism of iron-sulfur clusters in all domains of life.
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Proc Natl Acad Sci U S A, 107,
10412-10417.
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J.W.Chen,
C.M.Sun,
W.L.Sheng,
Y.C.Wang,
and
W.J.Syu
(2006).
Expression Analysis of Up-Regulated Genes Responding to Plumbagin in Escherichia coli.
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J Bacteriol, 188,
456-463.
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T.Ote,
M.Hashimoto,
Y.Ikeuchi,
M.Su'etsugu,
T.Suzuki,
T.Katayama,
and
J.Kato
(2006).
Involvement of the Escherichia coli folate-binding protein YgfZ in RNA modification and regulation of chromosomal replication initiation.
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Mol Microbiol, 59,
265-275.
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J.Kato
(2005).
Regulatory network of the initiation of chromosomal replication in Escherichia coli.
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Crit Rev Biochem Mol Biol, 40,
331-342.
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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.
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Links
