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PDBsum entry 1dw2
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Oxygen storage/transport
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PDB id
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1dw2
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Contents |
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* Residue conservation analysis
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PDB id:
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| Name: |
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Oxygen storage/transport
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Title:
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Structure of the nitric oxide complex of reduced shp, an oxygen binding cytochromE C
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Structure:
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CytochromE C. Chain: a, b, c
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Source:
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Rhodobacter sphaeroides. Organism_taxid: 1063
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Resolution:
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2.20Å
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R-factor:
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0.167
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R-free:
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0.229
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Authors:
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D.Leys,K.Backers,T.E.Meyer,W.R.Hagen,M.A.Cusanovich,J.J.Van Beeumen
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Key ref:
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D.Leys
et al.
(2000).
Crystal structures of an oxygen-binding cytochrome c from Rhodobacter sphaeroides.
J Biol Chem,
275,
16050-16056.
PubMed id:
DOI:
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Date:
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24-Jan-00
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Release date:
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28-Jun-00
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PROCHECK
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Headers
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References
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P81238
(SHP_RHOS4) -
Cytochrome c-type protein SHP from Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)
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Seq:
Struc:
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129 a.a.
113 a.a.
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Key: |
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Secondary structure |
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CATH domain |
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DOI no:
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J Biol Chem
275:16050-16056
(2000)
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PubMed id:
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Crystal structures of an oxygen-binding cytochrome c from Rhodobacter sphaeroides.
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D.Leys,
K.Backers,
T.E.Meyer,
W.R.Hagen,
M.A.Cusanovich,
J.J.Van Beeumen.
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ABSTRACT
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The photosynthetic bacterium Rhodobacter sphaeroides produces a heme protein
(SHP), which is an unusual c-type cytochrome capable of transiently binding
oxygen during autooxidation. Similar proteins have not only been observed in
other photosynthetic bacteria but also in the obligate methylotroph
Methylophilus methylotrophus and the metal reducing bacterium Shewanella
putrefaciens. A three-dimensional structure of SHP was derived using the
multiple isomorphous replacement phasing method. Besides a model for the
oxidized state (to 1.82 A resolution), models for the reduced state (2.1 A
resolution), the oxidized molecule liganded with cyanide (1. 90 A resolution),
and the reduced molecule liganded with nitric oxide (2.20 A resolution) could be
derived. The SHP structure represents a new variation of the class I cytochrome
c fold. The oxidized state reveals a novel sixth heme ligand, Asn(88), which
moves away from the iron upon reduction or when small molecules bind. The distal
side of the heme has a striking resemblance to other heme proteins that bind
gaseous compounds. In SHP the liberated amide group of Asn(88) stabilizes
solvent-shielded ligands through a hydrogen bond.
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Selected figure(s)
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Figure 1.
Fig. 1. . Alignment of the SHP from S. putrefaciens
(PHP), cytochrome c" of M. methylotrophus (16) (MHP), and SHP
from R. sphaeroides (12) (SHP). Heme ligands are colored red,
residues implicated in lining the distal heme pocket are blue,
the sixth heme ligand is green, and the two cysteines linked in
a disulfide bridge are yellow. Residues conserved in all three
sequences have been boxed.
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Figure 3.
Fig. 3. Ribbon diagrams of the oxidized SHP structure.
Heme is represented in fine bonds, and His47, Asn88, Cys89, and
Cys91 have been depicted by ball and sticks. This figure has
been generated using the programs MOLSCRIPT (41) and RASTER3D
(42).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2000,
275,
16050-16056)
copyright 2000.
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Figures were
selected
by an automated process.
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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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T.E.Meyer,
J.A.Kyndt,
and
M.A.Cusanovich
(2010).
Occurrence and sequence of Sphaeroides Heme Protein and diheme cytochrome C in purple photosynthetic bacteria in the family Rhodobacteraceae.
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BMC Biochem,
11,
24.
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C.J.Reedy,
M.M.Elvekrog,
and
B.R.Gibney
(2008).
Development of a heme protein structure-electrochemical function database.
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Nucleic Acids Res,
36,
D307-D313.
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F.J.Enguita,
E.Pohl,
D.L.Turner,
H.Santos,
and
M.A.Carrondo
(2006).
Structural evidence for a proton transfer pathway coupled with haem reduction of cytochrome c" from Methylophilus methylotrophus.
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J Biol Inorg Chem,
11,
189-196.
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PDB code:
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G.Van Driessche,
B.Devreese,
J.C.Fitch,
T.E.Meyer,
M.A.Cusanovich,
and
J.J.Van Beeumen
(2006).
GHP, a new c-type green heme protein from Halochromatium salexigens and other proteobacteria.
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FEBS J,
273,
2801-2811.
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I.N.Berezovsky,
W.W.Chen,
P.J.Choi,
and
E.I.Shakhnovich
(2005).
Entropic stabilization of proteins and its proteomic consequences.
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PLoS Comput Biol,
1,
e47.
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R.Bencheikh-Latmani,
S.M.Williams,
L.Haucke,
C.S.Criddle,
L.Wu,
J.Zhou,
and
B.M.Tebo
(2005).
Global transcriptional profiling of Shewanella oneidensis MR-1 during Cr(VI) and U(VI) reduction.
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Appl Environ Microbiol,
71,
7453-7460.
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D.M.Copeland,
A.H.West,
and
G.B.Richter-Addo
(2003).
Crystal structures of ferrous horse heart myoglobin complexed with nitric oxide and nitrosoethane.
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Proteins,
53,
182-192.
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PDB codes:
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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
code is
shown on the right.
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