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PDBsum entry 1crh
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Electron transport(cytochrome)
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PDB id
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1crh
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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 role of a conserved internal water molecule and its associated hydrogen bond network in cytochrome c.
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Authors
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A.M.Berghuis,
J.G.Guillemette,
G.Mclendon,
F.Sherman,
M.Smith,
G.D.Brayer.
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Ref.
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J Mol Biol, 1994,
236,
786-799.
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
96%.
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Abstract
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High resolution three-dimensional structures for the N52I and N52I-Y67F yeast
iso-1-cytochrome c variants have been completed in both oxidation states. The
most prominent structural difference observed in both mutant proteins is the
displacement of a conserved, internally bound water molecule (Wat166) from the
protein matrix. In wild-type yeast iso-1-cytochrome c the position and
orientation of this water molecule is found to be dependent on the oxidation
state of the heme iron atom. Overall our results suggest the function of Wat166
and its associated hydrogen bond network is threefold. First, the presence of
Wat166 provides a convenient mechanism to modify the hydrogen bond network
involving several residues near the Met80 ligand in an oxidation state dependent
manner. Second, Wat166 is necessary for the maintenance of the spatial
relationships between nearby side-chains and the hydrogen bond interactions
formed between these groups in this region of the protein. An essential part of
this role is ensuring the proper conformation of the side-chain of Tyr67 so that
it forms a hydrogen bond interaction with the heme ligand Met80. This hydrogen
bond influences the electron withdrawing power of the Met80 ligand and is
therefore a factor in controlling the midpoint reduction potential of cytochrome
c. Elimination of this interaction in the N52I-Y67F mutant protein or
elimination of Wat166 in the N52I protein with the subsequent disruption in the
position and interactions of the Tyr67 side-chain, leads to a drop of
approximately 56 mV in the observed midpoint reduction potential of the heme
group. Third, Wat166 also appears to mediate increases in the mobility of three
nearby segments of polypeptide chain when cytochrome c is in the oxidized state.
Previous studies have proposed these changes may be related to oxidation state
dependent interactions between cytochrome c and its redox partners. Coincident
with the absence of Wat166, such mobility changes are not observed in the N52I
and N52I-Y67F mutant proteins. It is possible that much of the increased protein
stability observed for both mutant proteins may be due to this factor. Finally,
our results show that neither heme iron charge nor heme plane distortion are
responsible for oxidation state dependent conformational changes in the pyrrole
A propionate region. Instead, the changes observed appear to be driven by the
change in conformation that the side-chain of Asn52 experiences as the result of
oxidation state dependent movement of Wat166.
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Secondary reference #1
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Title
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Mutation of tyrosine-67 to phenylalanine in cytochrome c significantly alters the local heme environment.
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Authors
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A.M.Berghuis,
J.G.Guillemette,
M.Smith,
G.D.Brayer.
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Ref.
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J Mol Biol, 1994,
235,
1326-1341.
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
89%.
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Secondary reference #2
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Title
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Effect of the asn52----Ile mutation on the redox potential of yeast cytochrome c. Theory and experiment.
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Authors
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R.Langen,
G.D.Brayer,
A.M.Berghuis,
G.Mclendon,
F.Sherman,
A.Warshel.
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Ref.
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J Mol Biol, 1992,
224,
589-600.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. A thermodynamic cycle that relates the redox
potentials of the native and the mutant ytochromes. Qred
and Q'''' designate the charges of the reduced and oxidized
states of he heme, espectively.
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Figure 4.
Figue 4. Drawings of the mmediate vicinity of (a)
Asn52 in wild-type yeast iso-1-cytochrome c and of (b)
Ile52 in the Asn52-+Ile mutant protein. Only the side-
chains f nearby residues are drawn, along with observed
hydrogen bonds (broken lines). Heme group atoms are
drawn with darker shading, and the pyrrole ring A
propionate group has been labeled. An internal water
molecule, Wat166, s shown s a larger sphere in the wild-
type protein, but is not present in the Asn52-+Ile mutant.
The side-chain of Asn52, through the orientation of its
dipole (see (a)) dstabilizes the oxidized form of the heme
group. Removal of this interaction in the mutat
Asn52-+lle protein results in a smaller destabilization of
the oxidized state and a corresponding decrease in
observed reduction potential.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #3
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Title
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Oxidation state-Dependent conformational changes in cytochrome c.
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Authors
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A.M.Berghuis,
G.D.Brayer.
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Ref.
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J Mol Biol, 1992,
223,
959-976.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. A schemtic representation of the atomic
skeleton of the heme group f cytochrome c and the atom
labeling convention used herein.
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Figure 10.
Figure 10. Drawings of the egion about the pyrrole
ing A propionate group in (a) reduced and (b) oxidized
yeast iso-l-cytochrome c, illustrating the positional shifts
nd altered hydrogen bonding patterns observed. The
yrrole ring A propionate group is hihlighted with dark
haded balls. Hydrogen bonds are indicated by hin
otted lines. The 2 internally bound water molecules,
Watl21 and -168, which mediate the interaction of Arg38
ith this heme propionate, are shown with largr spheres.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #4
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Title
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Enhanced thermodynamic stabilities of yeast iso-1-Cytochromes c with amino acid replacements at positions 52 and 102.
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Authors
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D.R.Hickey,
A.M.Berghuis,
G.Lafond,
J.A.Jaeger,
T.S.Cardillo,
D.Mclendon,
G.Das,
F.Sherman,
G.D.Brayer,
G.Mclendon.
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Ref.
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J Biol Chem, 1991,
266,
11686-11694.
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PubMed id
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Secondary reference #5
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Title
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Effects of reaction free energy in biological electron transfer in vitro and in vivo (in: electron transfer in inorganic, Organic, And biological systems)
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Authors
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G.McLendon,
D.R.Hickey,
A.M.Berghuis,
F.Sherman,
G.D.Brayer.
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Ref.
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adv chem ser, 1991,
228,
179.
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Secondary reference #6
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Title
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High-Resolution refinement of yeast iso-1-Cytochrome c and comparisons with other eukaryotic cytochromes c.
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Authors
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G.V.Louie,
G.D.Brayer.
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Ref.
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J Mol Biol, 1990,
214,
527-555.
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PubMed id
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Secondary reference #7
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Title
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Crystallization of yeast iso-2-Cytochrome c using a novel hair seeding technique.
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Authors
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C.J.Leung,
B.T.Nall,
G.D.Brayer.
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Ref.
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J Mol Biol, 1989,
206,
783-785.
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PubMed id
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