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PDBsum entry 1ib0
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Oxygen storage/transport
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PDB id
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1ib0
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.1.6.2.2
- cytochrome-b5 reductase.
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Reaction:
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2 Fe(III)-[cytochrome b5] + NADH = 2 Fe(II)-[cytochrome b5] + NAD+ + H+
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2
×
Fe(III)-[cytochrome b5]
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+
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NADH
Bound ligand (Het Group name = )
corresponds exactly
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=
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2
×
Fe(II)-[cytochrome b5]
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+
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NAD(+)
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+
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H(+)
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Cofactor:
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FAD
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FAD
Bound ligand (Het Group name =
FAD)
corresponds exactly
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Biochemistry
40:13574-13582
(2001)
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PubMed id:
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The structure and biochemistry of NADH-dependent cytochrome b5 reductase are now consistent.
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M.C.Bewley,
C.C.Marohnic,
M.J.Barber.
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ABSTRACT
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Cytochrome b5 reductase (cb5r) (EC 1.6.6.2) catalyzes the reduction of two
molecules of cytochrome b5 using NADH as the physiological electron donor. The
structure of pig cb5r at 2.4 A resolution was previously reported in the
literature, but it was inconsistent with the biochemistry; for example, K83 and
C245 were both implicated in the mechanism, but were not located at the active
site. To address this problem, we have determined the structures of cb5r from
rat at 2.0 A resolution and in a complex with NAD+ at 2.3 A resolution. We found
significant differences throughout the rat structure compared to that of pig,
including the locations of the lysine and cysteine residues mentioned above. To
test the structural models, we made single amino acid substitutions of this
lysine and showed that all substitutions produced correctly folded proteins and
exhibited normal flavin behavior. However, the apparent kcat(NADH) decreased,
and the apparent K(m) for NADH increased; the K(m)'s for cytochrome b5 were
unchanged relative to that of the wild type. The largest effect was for the
glutamate-substituted protein, which was further characterized using a charge
transfer assay and found to be less efficient at NADH utilization than the wild
type. These results are consistent with a role for this lysine in stabilizing
the NADH-bound form of cb5r. We have concluded that the pig structure was
mistraced in several regions and have reinterpreted mutants in these regions
that give rise to the hereditary disease methemoglobinemia.
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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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M.Medina
(2009).
Structural and mechanistic aspects of flavoproteins: photosynthetic electron transfer from photosystem I to NADP+.
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FEBS J,
276,
3942-3958.
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J.R.Kurian,
B.J.Longlais,
and
L.A.Trepanier
(2007).
Discovery and characterization of a cytochrome b5 variant in humans with impaired hydroxylamine reduction capacity.
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Pharmacogenet Genomics,
17,
597-603.
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S.Kim,
M.Suga,
K.Ogasahara,
T.Ikegami,
Y.Minami,
T.Yubisui,
and
T.Tsukihara
(2007).
Structure of Physarum polycephalum cytochrome b5 reductase at 1.56 A resolution.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
63,
274-279.
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PDB code:
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T.Ikegami,
E.Kameyama,
S.Y.Yamamoto,
Y.Minami,
and
T.Yubisui
(2007).
Structure and properties of the recombinant NADH-cytochrome b5 reductase of Physarum polycephalum.
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Biosci Biotechnol Biochem,
71,
783-790.
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D.H.Hyun,
J.O.Hernandez,
M.P.Mattson,
and
R.de Cabo
(2006).
The plasma membrane redox system in aging.
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Ageing Res Rev,
5,
209-220.
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M.J.Percy,
L.J.Crowley,
C.A.Davis,
M.F.McMullin,
G.Savage,
J.Hughes,
C.McMahon,
R.J.Quinn,
O.Smith,
M.J.Barber,
and
T.R.Lappin
(2005).
Recessive congenital methaemoglobinaemia: functional characterization of the novel D239G mutation in the NADH-binding lobe of cytochrome b5 reductase.
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Br J Haematol,
129,
847-853.
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M.J.Percy,
N.V.McFerran,
and
T.R.Lappin
(2005).
Disorders of oxidised haemoglobin.
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Blood Rev,
19,
61-68.
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K.Panda,
S.Adak,
D.Konas,
M.Sharma,
and
D.J.Stuehr
(2004).
A conserved aspartate (Asp-1393) regulates NADPH reduction of neuronal nitric-oxide synthase: implications for catalysis.
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J Biol Chem,
279,
18323-18333.
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S.Bando,
T.Takano,
T.Yubisui,
K.Shirabe,
M.Takeshita,
and
A.Nakagawa
(2004).
Structure of human erythrocyte NADH-cytochrome b5 reductase.
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Acta Crystallogr D Biol Crystallogr,
60,
1929-1934.
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PDB code:
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D.Grabowska,
D.Plochocka,
E.Jablonska-Skwiecinska,
A.Chelstowska,
I.Lewandowska,
K.Staniszewska,
Z.Majewska,
I.Witos,
and
B.Burzynska
(2003).
Compound heterozygosity of two missense mutations in the NADH-cytochrome b5 reductase gene of a Polish patient with type I recessive congenital methaemoglobinaemia.
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Eur J Haematol,
70,
404-409.
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M.H.Hefti,
J.Vervoort,
and
W.J.van Berkel
(2003).
Deflavination and reconstitution of flavoproteins.
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Eur J Biochem,
270,
4227-4242.
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S.Kimura,
M.Kawamura,
and
T.Iyanagi
(2003).
Role of Thr(66) in porcine NADH-cytochrome b5 reductase in catalysis and control of the rate-limiting step in electron transfer.
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J Biol Chem,
278,
3580-3589.
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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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Links
