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PDBsum entry 1aaz
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Electron transport
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PDB id
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1aaz
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structure of oxidized bacteriophage t4 glutaredoxin (thioredoxin). Refinement of native and mutant proteins.
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Authors
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H.Eklund,
M.Ingelman,
B.O.Söderberg,
T.Uhlin,
P.Nordlund,
M.Nikkola,
U.Sonnerstam,
T.Joelson,
K.Petratos.
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Ref.
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J Mol Biol, 1992,
228,
596-618.
[DOI no: ]
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PubMed id
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Abstract
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The structure of wild-type bacteriophage T4 glutaredoxin (earlier called
thioredoxin) in its oxidized form has been refined in a monoclinic crystal form
at 2.0 A resolution to a crystallographic R-factor of 0.209. A mutant T4
glutaredoxin gives orthorhombic crystals of better quality. The structure of
this mutant has been solved by molecular replacement methods and refined at 1.45
A to an R-value of 0.175. In this mutant glutaredoxin, the active site residues
Val15 and Tyr16 have been substituted by Gly and Pro, respectively, to mimic
that of Escherichia coli thioredoxin. The main-chain conformation of the
wild-type protein is similar in the two independently determined molecules in
the asymmetric unit of the monoclinic crystals. On the other hand, side-chain
conformations differ considerably between the two molecules due to heterologous
packing interactions in the crystals. The structure of the mutant protein is
very similar to the wild-type protein, except at mutated positions and at parts
involved in crystal contacts. The active site disulfide bridge between Cys14 and
Cys17 is located at the first turn of helix alpha 1. The torsion angles of these
residues are similar to those of Escherichia coli thioredoxin. The torsion angle
around the S-S bond is smaller than that normally observed for disulfides: 58
degrees, 67 degrees and 67 degrees for wild-type glutaredoxin molecule A and B
and mutant glutaredoxin, respectively. Each sulfur atom of the disulfide
cysteines in T4 glutaredoxin forms a hydrogen bond to one main-chain nitrogen
atom. The active site is shielded from solvent on one side by the beta-carbon
atoms of the cysteine residues plus side-chains of residues 7, 9, 21 and 33.
From the opposite side, there is a cleft where the sulfur atom of Cys14 is
accessible and can be attacked by a nucleophilic thiolate ion in the initial
step of the reduction reaction.
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Figure 4.
Figure 4. Electon density maps of mutant glutaredoxi. The electron density 2(F,j -IF,1 contoured at la for (a) a
normal tyrosine Tyr7) and (b) Tyr85 for which the elecron density map indicates 2 conformations, (c) for a normal
leucine (Leu85) and (d) the ensity for Leu55 indicating 2 conformations. Both conformations have been treated as haf
occupied and no attempts hae ben made to refine the occupancies of the individual conformations.
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Figure 7.
Figure 7. Hydrogen bonding scheme. Schematic
drawing of the main-chain hydrogen bonding in T4 gluta-
redoxin. According to normal conventions, we have
assigned a hydrogen bond whn donor and acceptor
atoms are closer than 3.3 A.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1992,
228,
596-618)
copyright 1992.
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Secondary reference #1
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Title
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Three-Dimensional structure of thioredoxin induced by bacteriophage t4.
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Authors
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B.O.Söderberg,
B.M.Sjöberg,
U.Sonnerstam,
C.I.Brändén.
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Ref.
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Proc Natl Acad Sci U S A, 1978,
75,
5827-5830.
[DOI no: ]
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PubMed id
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Secondary reference #2
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Title
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Thioredoxin induced by bacteriophage t4: crystallization and preliminary crystallographic data.
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Authors
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B.M.Sjöberg,
B.O.Söderberg.
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Ref.
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J Mol Biol, 1976,
100,
415-419.
[DOI no: ]
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PubMed id
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Figure 1.
FIG. 1. A rystal of T4 thioredoxin obtained in 0.020 M-bistris propane uffer (pH 6.80) contain-
ing 0-001 .-Od 2+ an 24% ethanol. The axis of the crystal is about 2 ram.
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Figure 2.
Fin 2. A 160 ~ precession photograph of the hk0 projection of T4thioredoxin. Exposure time
11-5 h using a load of 1.0 kW on a fine focus sealed X-ray tube.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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