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PDBsum entry 1v4k
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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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Crystal structure of octaprenyl pyrophosphate synthase from hyperthermophilic thermotoga maritima and mechanism of product chain length determination.
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Authors
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R.T.Guo,
C.J.Kuo,
C.C.Chou,
T.P.Ko,
H.L.Shr,
P.H.Liang,
A.H.Wang.
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Ref.
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J Biol Chem, 2004,
279,
4903-4912.
[DOI no: ]
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PubMed id
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Abstract
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Octaprenyl pyrophosphate synthase (OPPs) catalyzes consecutive condensation
reactions of farnesyl pyrophosphate (FPP) with isopentenyl pyrophosphate (IPP)
to generate C40 octaprenyl pyrophosphate (OPP), which constitutes the side chain
of bacterial ubiquinone or menaquinone. In this study, the first structure of
long chain C40-OPPs from Thermotoga maritima has been determined to 2.28-A
resolution. OPPs is composed entirely of alpha-helices joined by connecting
loops and is arranged with nine core helices around a large central cavity. An
elongated hydrophobic tunnel between D and F alpha-helices contains two DDXXD
motifs on the top for substrate binding and is occupied at the bottom with two
large residues Phe-52 and Phe-132. The products of the mutant F132A OPPs are
predominantly C50, longer than the C40 synthesized by the wild-type and F52A
mutant OPPs, suggesting that Phe-132 is the key residue for determining the
product chain length. Ala-76 and Ser-77 located close to the FPP binding site
and Val-73 positioned further down the tunnel were individually mutated to
larger amino acids. A76Y and S77F mainly produce C20 indicating that the mutated
large residues in the vicinity of the FPP site limit the substrate chain
elongation. Ala-76 is the fifth amino acid upstream from the first DDXXD motif
on helix D of OPPs, and its corresponding amino acid in FPPs is Tyr. In
contrast, V73Y mutation led to additional accumulation of C30 intermediate. The
new structure of the trans-type OPPs, together with the recently determined
cis-type UPPs, significantly extends our understanding on the biosynthesis of
long chain polyprenyl molecules.
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Figure 3.
FIG. 3. OPPs active site structure and reaction mechanism.
In A, the surface of active site is color coded from red to blue
according to charge potential from -15 to 15 k[B]T. This figure
was generated using GRASP (30). In B, two sulfate ions in the
active site of totally six sulfates of OPPs F132A mutant are
shown (these sulfate ions are more obvious than other data
sets). Along with two sulfate ions, amino acids Lys-41, Arg-44,
His-74, Asp-81, Asp-82, Asp-85, Arg-90, Arg-91, Asp-204,
Asp-205, and Asp-208 are shown in ball-and-stick model. S1
containing the first DDXXD motif is responsible for binding with
FPP, and S2 located downstream the FPP binding site functions to
stabilize the PP[i] leaving group. This is illustrated in C that
Arg-90 and Arg-91 are important in FPP binding, and AArg-44,
Lys-41, and His-74 surround another sulfate ion to grasp the
leaving group of FPP while reaction occurs.
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Figure 8.
FIG. 8. Proposed mechanism for chain length determination
catalyzed by OPPs. The first DDXXD motif attached to helix D
represents the FPP binding site. Ser-77 and Ala-76 are located
in immediate proximity of FPP, and V73Y is further down. The
substitution of Ser-77 and Ala-76 with larger residues led to
the formation of C[20], a single condensation between the bound
FPP and IPP. V73Y mutation results in temporary accumulation of
C[30]. Phe-132 located on the bottom of helix D blocks further
chain elongation of OPP and determines the ultimate product
chain length.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2004,
279,
4903-4912)
copyright 2004.
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Secondary reference #1
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Title
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Preliminary X-Ray diffraction analysis of octaprenyl pyrophosphate synthase crystals from thermotoga maritima and escherichia coli.
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Authors
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R.T.Guo,
T.P.Ko,
C.C.Chou,
H.L.Shr,
H.M.Chu,
Y.H.Tsai,
P.H.Liang,
A.H.Wang.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2003,
59,
2265-2268.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
96%.
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Figure 2.
Figure 2 Crystals of octaprenyl pyrophosphate synthase (OPPs)
from T. maritima (a) and E. coli (b) used in data collection;
the approximate dimensions of the crystals are (a) 0.5 × 0.5 ×
0.2 mm and (b) 0.7 × 0.3 × 0.1 mm.
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The above figure is
reproduced from the cited reference
with permission from the IUCr
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