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PDBsum entry 1jeh
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Oxidoreductase
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PDB id
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1jeh
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Contents |
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* Residue conservation analysis
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PDB id:
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Oxidoreductase
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Title:
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Crystal structure of yeast e3, lipoamide dehydrogenase
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Structure:
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Dihydrolipoamide dehydrogenase. Chain: a, b. Ec: 1.8.1.4
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Source:
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Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
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Biol. unit:
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Dimer (from
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Resolution:
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2.40Å
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R-factor:
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0.202
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R-free:
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0.260
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Authors:
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T.Toyoda,K.Suzuki,T.Sekigushi,J.Reed,A.Takenaka
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Key ref:
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T.Toyoda
et al.
(1998).
Crystal structure of eucaryotic E3, lipoamide dehydrogenase from yeast.
J Biochem (tokyo),
123,
668-674.
PubMed id:
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Date:
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18-Jun-01
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Release date:
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11-Jul-01
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PROCHECK
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Headers
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References
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P09624
(DLDH_YEAST) -
Dihydrolipoyl dehydrogenase, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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Seq:
Struc:
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499 a.a.
478 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Enzyme class:
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E.C.1.8.1.4
- dihydrolipoyl dehydrogenase.
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Pathway:
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Glycine Cleavage System
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Reaction:
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N6-[(R)-dihydrolipoyl]-L-lysyl-[protein] + NAD+ = N6-[(R)-lipoyl]- L-lysyl-[protein] + NADH + H+
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N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein]
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+
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NAD(+)
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=
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N(6)-[(R)-lipoyl]- L-lysyl-[protein]
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+
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NADH
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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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J Biochem (tokyo)
123:668-674
(1998)
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PubMed id:
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Crystal structure of eucaryotic E3, lipoamide dehydrogenase from yeast.
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T.Toyoda,
K.Suzuki,
T.Sekiguchi,
L.J.Reed,
A.Takenaka.
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ABSTRACT
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The crystal structure of eucaryotic lipoamide dehydrogenase from yeast has been
determined by an X-ray analysis at 2.7 (partially at 2.4) A resolution. The
enzyme has two identical subunits related by a pseudo twofold symmetry. The
tertiary structure is similar to those of other procaryotic enzymes. The active
site, consisting of FAD, Cys44, and Cys49 from one subunit and His457' from the
other subunit, is highly conserved. This enzyme is directly bound to the core
protein E2 of the 2-oxoglutarate dehydrogenase complex, whereas it is bound to
the pyruvate dehydrogenase complex through a protein X. The calculated
electrostatic potential suggests two characteristic regions for binding with
these two proteins.
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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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B.E.Keyes,
and
D.J.Burke
(2009).
Irc15 Is a microtubule-associated protein that regulates microtubule dynamics in Saccharomyces cerevisiae.
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Curr Biol,
19,
472-478.
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T.Nakai,
S.Kuramitsu,
and
N.Kamiya
(2008).
Structural bases for the specific interactions between the E2 and E3 components of the Thermus thermophilus 2-oxo acid dehydrogenase complexes.
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J Biochem,
143,
747-758.
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N.K.Lokanath,
C.Kuroishi,
N.Okazaki,
and
N.Kunishima
(2004).
Purification, crystallization and preliminary crystallographic analysis of the glycine-cleavage system component T-protein from Pyrococcus horikoshii OT3.
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Acta Crystallogr D Biol Crystallogr,
60,
1450-1452.
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T.Nakai,
J.Ishijima,
R.Masui,
S.Kuramitsu,
and
N.Kamiya
(2003).
Structure of Thermus thermophilus HB8 H-protein of the glycine-cleavage system, resolved by a six-dimensional molecular-replacement method.
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Acta Crystallogr D Biol Crystallogr,
59,
1610-1618.
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PDB code:
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T.Nakai,
N.Nakagawa,
N.Maoka,
R.Masui,
S.Kuramitsu,
and
N.Kamiya
(2003).
Coexpression, purification, crystallization and preliminary X-ray characterization of glycine decarboxylase (P-protein) of the glycine-cleavage system from Thermus thermophilus HB8.
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Acta Crystallogr D Biol Crystallogr,
59,
554-557.
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K.Suzuki,
W.Adachi,
N.Yamada,
M.Tsunoda,
K.Koike,
M.Koike,
T.Sekiguchi,
and
A.Takénaka
(2002).
Crystallization and preliminary X-ray analysis of the full-size cubic core of pig 2-oxoglutarate dehydrogenase complex.
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Acta Crystallogr D Biol Crystallogr,
58,
833-835.
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A.W.Munro,
P.Taylor,
and
M.D.Walkinshaw
(2000).
Structures of redox enzymes.
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Curr Opin Biotechnol,
11,
369-376.
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M.Faure,
J.Bourguignon,
M.Neuburger,
D.MacHerel,
L.Sieker,
R.Ober,
R.Kahn,
C.Cohen-Addad,
and
R.Douce
(2000).
Interaction between the lipoamide-containing H-protein and the lipoamide dehydrogenase (L-protein) of the glycine decarboxylase multienzyme system 2. Crystal structures of H- and L-proteins.
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Eur J Biochem,
267,
2890-2898.
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PDB codes:
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K.F.Sheu,
and
J.P.Blass
(1999).
The alpha-ketoglutarate dehydrogenase complex.
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Ann N Y Acad Sci,
893,
61-78.
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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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