 |
PDBsum entry 1csv
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Electron transport(heme protein)
|
PDB id
|
|
|
|
1csv
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Replacements in a conserved leucine cluster in the hydrophobic heme pocket of cytochrome c.
|
|
|
Authors
|
|
T.P.Lo,
M.E.Murphy,
J.G.Guillemette,
M.Smith,
G.D.Brayer.
|
|
|
Ref.
|
|
Protein Sci, 1995,
4,
198-208.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
A cluster of highly conserved leucine side chains from residues 9, 68, 85, 94,
and 98 is located in the hydrophobic heme pocket of cytochrome c. The
contributions of two of these, Leu 85 and Leu 94, have been studied using a
protein structure-function-mutagenesis approach to probe their roles in the
maintenance of overall structural integrity and electron transfer activity.
Structural studies of the L85C, L85F, L85M, and L94S mutant proteins show that,
in each case, the overall fold of cytochrome c is retained, but that localized
conformational shifts are required to accommodate the introduced side chains. In
particular, the side chains of Cys 85 and Phe 85 form energetically favorable
interactions with Phe 82, whereas Met 85 takes on a more remote conformation to
prevent an unfavorable interaction with the phenyl ring of Phe 82. In the case
of the L94S mutant protein, the new polar group introduced is found to form
hydrogen bonds to nearby carbonyl groups. In all proteins with substitutions at
Leu 85, the hydrophobic nature of the heme pocket is preserved and no
significant decrease in heme reduction potential is observed. Despite earlier
predictions that Leu 85 is an important determinant in cytochrome c electron
transfer partner complexation, our studies show this is unlikely to be the case
because the considerable surface contour perturbations made by substitutions at
this residue do not correspondingly translate into significant changes in
electron transfer rates. For the L94S mutant protein, the substitution of a
polar hydroxyl group directly into the hydrophobic heme pocket has a larger
effect on heme reduction potential, but this is mitigated by two factors. First,
the side chain of Ser 94 is rotated away from the heme group and, second, the
side chain of Leu 98 shifts into a portion of the new space available, partially
shielding the heme group. The Leu 94 Ser substitution does not perturb the
highly conserved interface formed by the nearly perpendicular packing of the N-
and C-terminal helices of cytochrome c, ruling this out as the cause of this
mutant protein becoming thermally labile and having a lower functional activity.
Our results show these effects are most likely attributable to disruption of the
heme pocket region. Much of the ability of cytochrome c to absorb the
introduction of mutations at Leu 85 and Leu 94 appears to be a consequence of
the conformational flexibility afforded by the leucine cluster in this region as
well as the presence of a nearby internal cavity.(ABSTRACT TRUNCATED AT 400
WORDS)
|
|
|
|
|
|
|
|
Figure 4.
Fig. 4. Stereo iagra showing the region about
Leu 94 intheL94Smutant protein. Thestructure of
thewild-typeproteinhasbeensuperimposed and is
shown withthick lines, whereasthemutantprotein
structureisdepicted by thin lines. Altered side-chain
conformations for Leu 9 andLeu98areclearly evi-
dent. Hydrogen bonds formedbetweenthehydroxyl
group of Ser94andthe main-chain carbonyl oxygen
atos of Asp 90 andArg91arerepresentedbydashed
lines. Intrahelicalhydrogen bonds formedbetween
thesecarbonyl groups and theamidenitrogen atoms
of Leu 94 and Ile 95 are also epresntedbydashed
lines.
|
|
Figure 5.
Fig. 5. Stereo diagram showing the location f
thehydrophobicinternal cavity (dot surface)
found in wild-type iso-1 cytochrome c. he
heme group and nearby side chains that define
the outer limits of this cavityin the L85F (thick
lines) nd L94S (thin lines) mutant proteins
havebeen superimposed onthe structure of te
wild-type protein (medium lines). The differ-
ent conformations observed for he Leu98 side
chain are largely responsible for determining
the size ofthis internal cavity. In the L85F mu-
tant protein,the Leu 98 side chain moves into
theinternal cavity, effectively eliminating this
feature. In the L94S mutant protein, the Leu98
side chain moves toward the side chain of Ser 94,
causing n increase in cavity size. The volume
and surface area of this in a wide range
of mutantprotins is tabulated in Table 5.
|
|
|
|
|
|
The above figures are
reprinted
from an Open Access publication published by the Protein Society:
Protein Sci
(1995,
4,
198-208)
copyright 1995.
|
|
|
Secondary reference #1
|
|
|
Title
|
|
Structural studies of the roles of residues 82 and 85 at the interactive face of cytochrome c.
|
|
|
Authors
|
|
T.P.Lo,
J.G.Guillemette,
G.V.Louie,
M.Smith,
G.D.Brayer.
|
|
|
Ref.
|
|
Biochemistry, 1995,
34,
163-171.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #2
|
|
|
Title
|
|
Oxidation state-Dependent conformational changes in cytochrome c.
|
|
|
Authors
|
|
A.M.Berghuis,
G.D.Brayer.
|
|
|
Ref.
|
|
J Mol Biol, 1992,
223,
959-976.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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.
|
|
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.
|
|
|
|
|
|
The above figures are
reproduced from the cited reference
with permission from Elsevier
|
|
|
Secondary reference #3
|
|
|
Title
|
|
High-Resolution refinement of yeast iso-1-Cytochrome c and comparisons with other eukaryotic cytochromes c.
|
|
|
Authors
|
|
G.V.Louie,
G.D.Brayer.
|
|
|
Ref.
|
|
J Mol Biol, 1990,
214,
527-555.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #4
|
|
|
Title
|
|
A polypeptide chain-Refolding event occurs in the gly82 variant of yeast iso-1-Cytochrome c.
|
|
|
Authors
|
|
G.V.Louie,
G.D.Brayer.
|
|
|
Ref.
|
|
J Mol Biol, 1989,
210,
313-322.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #5
|
|
|
Title
|
|
Crystallization of yeast iso-2-Cytochrome c using a novel hair seeding technique.
|
|
|
Authors
|
|
C.J.Leung,
B.T.Nall,
G.D.Brayer.
|
|
|
Ref.
|
|
J Mol Biol, 1989,
206,
783-785.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #6
|
|
|
Title
|
|
Yeast iso-1-Cytochrome c. A 2.8 a resolution three-Dimensional structure determination.
|
|
|
Authors
|
|
G.V.Louie,
W.L.Hutcheon,
G.D.Brayer.
|
|
|
Ref.
|
|
J Mol Biol, 1988,
199,
295-314.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #7
|
|
|
Title
|
|
Role of phenylalanine-82 in yeast iso-1-Cytochrome c and remote conformational changes induced by a serine residue at this position.
|
|
|
Authors
|
|
G.V.Louie,
G.J.Pielak,
M.Smith,
G.D.Brayer.
|
|
|
Ref.
|
|
Biochemistry, 1988,
27,
7870-7876.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
|
