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Oxidoreductase
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PDB id
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1biq
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* Residue conservation analysis
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Enzyme class:
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E.C.1.17.4.1
- Ribonucleoside-diphosphate reductase.
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Reaction:
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2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin
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2'-deoxyribonucleoside diphosphate
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+
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thioredoxin disulfide
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+
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H(2)O
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=
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ribonucleoside diphosphate
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+
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thioredoxin
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Cofactor:
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Iron
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Gene Ontology (GO) functional annotation
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Cellular component
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cytoplasm
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3 terms
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Biological process
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oxidation reduction
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5 terms
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Biochemical function
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protein binding
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6 terms
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DOI no:
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Biochemistry
37:10798-10807
(1998)
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PubMed id:
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Crystal structures of two self-hydroxylating ribonucleotide reductase protein R2 mutants: structural basis for the oxygen-insertion step of hydroxylation reactions catalyzed by diiron proteins.
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D.T.Logan,
F.deMaré,
B.O.Persson,
A.Slaby,
B.M.Sjöberg,
P.Nordlund.
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ABSTRACT
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The R2 protein of ribonucleotide reductase catalyzes the dioxygen-dependent
one-electron oxidation of Tyr122 at a diiron-carboxylate site. Methane
monooxygenase and related hydroxylases catalyze hydrocarbon hydroxylation at
diiron sites structurally related to the one in R2. In protein R2, the likely
reaction site for dioxygen is close to Phe208. The crystal structure of an iron
ligand mutant R2, Y122F/E238A, reveals the hydroxylation of Phe208 at the meta,
or epsilon-, ring position and the subsequent coordination of this residue to
the diiron site. In another mutant, F208Y, the "foreign" residue
Tyr208 is hydroxylated to Dopa. The structures of apo and diferrous F208Y
presented here suggest that Tyr208 is coordinated to the iron site of F208Y
throughout the Dopa generation cycle. Together, the structural data on these two
mutants suggest two possible reaction geometries for the hydroxylation reaction
catalyzed by these modified R2 diiron sites, geometries which might be relevant
for the hydroxylation reaction catalyzed by other diiron sites such as methane
monooxygenase. A critical role for residue Glu238 in directing the oxidative
power of the reactive intermediate toward oxidation of Tyr122 is proposed.
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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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E.R.Farquhar,
J.P.Emerson,
K.D.Koehntop,
M.F.Reynolds,
M.Trmčić,
and
L.Que
(2011).
In vivo self-hydroxylation of an iron-substituted manganese-dependent extradiol cleaving catechol dioxygenase.
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J Biol Inorg Chem, 16,
589-597.
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C.B.Bell,
J.R.Calhoun,
E.Bobyr,
P.P.Wei,
B.Hedman,
K.O.Hodgson,
W.F.Degrado,
and
E.I.Solomon
(2009).
Spectroscopic definition of the biferrous and biferric sites in de novo designed four-helix bundle DFsc peptides: implications for O2 reactivity of binuclear non-heme iron enzymes.
|
| |
Biochemistry, 48,
59-73.
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C.S.Andersson,
and
M.Högbom
(2009).
A Mycobacterium tuberculosis ligand-binding Mn/Fe protein reveals a new cofactor in a remodeled R2-protein scaffold.
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Proc Natl Acad Sci U S A, 106,
5633-5638.
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PDB code:
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K.D.Koehntop,
S.Marimanikkuppam,
M.J.Ryle,
R.P.Hausinger,
and
L.Que
(2006).
Self-hydroxylation of taurine/alpha-ketoglutarate dioxygenase: evidence for more than one oxygen activation mechanism.
|
| |
J Biol Inorg Chem, 11,
63-72.
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|
|
J.R.Calhoun,
F.Nastri,
O.Maglio,
V.Pavone,
A.Lombardi,
and
W.F.DeGrado
(2005).
Artificial diiron proteins: from structure to function.
|
| |
Biopolymers, 80,
264-278.
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M.Bennati,
F.Lendzian,
M.Schmittel,
and
H.Zipse
(2005).
Spectroscopic and theoretical approaches for studying radical reactions in class I ribonucleotide reductase.
|
| |
Biol Chem, 386,
1007-1022.
|
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M.Kolberg,
D.T.Logan,
G.Bleifuss,
S.Pötsch,
B.M.Sjöberg,
A.Gräslund,
W.Lubitz,
G.Lassmann,
and
F.Lendzian
(2005).
A new tyrosyl radical on Phe208 as ligand to the diiron center in Escherichia coli ribonucleotide reductase, mutant R2-Y122H. Combined x-ray diffraction and EPR/ENDOR studies.
|
| |
J Biol Chem, 280,
11233-11246.
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PDB code:
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M.J.Ryle,
K.D.Koehntop,
A.Liu,
L.Que,
and
R.P.Hausinger
(2003).
Interconversion of two oxidized forms of taurine/alpha-ketoglutarate dioxygenase, a non-heme iron hydroxylase: evidence for bicarbonate binding.
|
| |
Proc Natl Acad Sci U S A, 100,
3790-3795.
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|
O.Maglio,
F.Nastri,
V.Pavone,
A.Lombardi,
and
W.F.DeGrado
(2003).
Preorganization of molecular binding sites in designed diiron proteins.
|
| |
Proc Natl Acad Sci U S A, 100,
3772-3777.
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|
PDB code:
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|
|
E.N.Marsh,
and
W.F.DeGrado
(2002).
Noncovalent self-assembly of a heterotetrameric diiron protein.
|
| |
Proc Natl Acad Sci U S A, 99,
5150-5154.
|
|
|
|
|
|
|
M.J.Ryle,
and
R.P.Hausinger
(2002).
Non-heme iron oxygenases.
|
| |
Curr Opin Chem Biol, 6,
193-201.
|
|
|
|
|
|
|
C.M.Summa,
A.Lombardi,
M.Lewis,
and
W.F.DeGrado
(1999).
Tertiary templates for the design of diiron proteins.
|
| |
Curr Opin Struct Biol, 9,
500-508.
|
|
|
|
|
|
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
code is
shown on the right.
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|
Links
