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PDBsum entry 3m3b
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Oxygen transport
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PDB id
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3m3b
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Contents |
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* Residue conservation analysis
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Proc Natl Acad Sci U S A
107:8581-8586
(2010)
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PubMed id:
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Roles of glutamates and metal ions in a rationally designed nitric oxide reductase based on myoglobin.
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Y.W.Lin,
N.Yeung,
Y.G.Gao,
K.D.Miner,
S.Tian,
H.Robinson,
Y.Lu.
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ABSTRACT
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A structural and functional model of bacterial nitric oxide reductase (NOR) has
been designed by introducing two glutamates (Glu) and three histidines (His) in
sperm whale myoglobin. X-ray structural data indicate that the three His and one
Glu (V68E) residues bind iron, mimicking the putative Fe(B) site in NOR, while
the second Glu (I107E) interacts with a water molecule and forms a hydrogen
bonding network in the designed protein. Unlike the first Glu (V68E), which
lowered the heme reduction potential by approximately 110 mV, the second Glu has
little effect on the heme potential, suggesting that the negatively charged Glu
has a different role in redox tuning. More importantly, introducing the second
Glu resulted in a approximately 100% increase in NOR activity, suggesting the
importance of a hydrogen bonding network in facilitating proton delivery during
NOR reactivity. In addition, EPR and X-ray structural studies indicate that the
designed protein binds iron, copper, or zinc in the Fe(B) site, each with
different effects on the structures and NOR activities, suggesting that both
redox activity and an intermediate five-coordinate heme-NO species are important
for high NOR activity. The designed protein offers an excellent model for NOR
and demonstrates the power of using designed proteins as a simpler and more
well-defined system to address important chemical and biological issues.
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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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Y.Matsumoto,
T.Tosha,
A.V.Pisliakov,
T.Hino,
H.Sugimoto,
S.Nagano,
Y.Sugita,
and
Y.Shiro
(2012).
Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus.
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Nat Struct Mol Biol,
19,
238-245.
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PDB codes:
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T.Li,
H.L.Bonkovsky,
and
J.T.Guo
(2011).
Structural analysis of heme proteins: implications for design and prediction.
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BMC Struct Biol,
11,
13.
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Y.W.Lin
(2011).
Structural insights into a low-spin myoglobin variant with bis-histidine coordination from molecular modeling.
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Proteins,
79,
679-684.
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S.Lutz
(2010).
Beyond directed evolution--semi-rational protein engineering and design.
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Curr Opin Biotechnol,
21,
734-743.
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T.Hino,
Y.Matsumoto,
S.Nagano,
H.Sugimoto,
Y.Fukumori,
T.Murata,
S.Iwata,
and
Y.Shiro
(2010).
Structural basis of biological N2O generation by bacterial nitric oxide reductase.
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Science,
330,
1666-1670.
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PDB code:
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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.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
