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PDBsum entry 2fg7
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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 and catalytic mechanism of a novel n-Succinyl-L-Ornithine transcarbamylase in arginine biosynthesis of bacteroides fragilis.
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Authors
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D.Shi,
H.Morizono,
J.Cabrera-Luque,
X.Yu,
L.Roth,
M.H.Malamy,
N.M.Allewell,
M.Tuchman.
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Ref.
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J Biol Chem, 2006,
281,
20623-20631.
[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 have
been manually determined.
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Abstract
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A Bacteroides fragilis gene (argF'(bf)), the disruption of which renders the
bacterium auxotrophic for arginine, was expressed and its recombinant protein
purified and studied. The novel protein catalyzes the carbamylation of
N-succinyl-L-ornithine but not L-ornithine or N-acetyl-L-ornithine, forming
N-succinyl-L-citrulline. Crystal structures of this novel transcarbamylase
complexed with carbamyl phosphate and N-succinyl-L-norvaline, as well as sulfate
and N-succinyl-L-norvaline have been determined and refined to 2.9 and 2.8 A
resolution, respectively. They provide structural evidence that this protein is
a novel N-succinyl-L-ornithine transcarbamylase. The data provided herein
suggest that B. fragilis uses N-succinyl-L-ornithine rather than
N-acetyl-L-ornithine for de novo arginine biosynthesis and therefore that this
pathway in Bacteroides is different from the canonical arginine biosynthetic
pathway of most organisms. Comparison of the structures of the new protein with
those recently reported for N-acetyl-L-ornithine transcarbamylase indicates that
amino acid residue 90 (B. fragilis numbering) plays an important role in
conferring substrate specificity for N-succinyl-L-ornithine versus
N-acetyl-L-ornithine. Movement of the 120 loop upon substrate binding occurs in
N-succinyl-L-ornithine transcarbamylase, while movement of the 80 loop and
significant domain closure take place as in other transcarbamylases. These
findings provide new information on the putative role of succinylated
intermediates in arginine biosynthesis and on the evolution of transcarbamylases.
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Figure 1.
Contours of the electron density maps (2F[o] - F[c]) (1.0 σ
shown in blue cage) at 2.8 and 2.9 Å resolution for the
SO[4]+SNO-bound (left) and CP+SNO-bound structures (right),
respectively.
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Figure 4.
Active site of SOTCase. The final refined positions of the
ligands are represented as colored sticks. A, stereo view
showing the active site of B. fragilis CP+SNO-bound SOTCase.
Interactions of active site residues with bound CP and SNO
(yellow stick) are illustrated in pink dashed lines. Residue
Trp^75 indicated by ^* is from an adjacent monomer. B,
comparison of the active sites of SOTCase (left) and AOTCase
(right) near the succinyl group. SNO and N-acetylcitrulline are
shown as thick ball-and-stick models, while the surrounding
residues are shown as thin ball-and-stick models. Residue Pro^90
in SOTCase from the adjacent subunit (equivalent to Glu^92 in
AOTCase) shown in red is the residue that distinguishes SOTCase
from AOTCase. Coordinates of AOTCase are taken from PDB 1YH1.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2006,
281,
20623-20631)
copyright 2006.
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