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PDBsum entry 1u1v
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Isomerase, lyase
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PDB id
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1u1v
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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 function of the phenazine biosynthetic protein phzf from pseudomonas fluorescens.
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Authors
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W.Blankenfeldt,
A.P.Kuzin,
T.Skarina,
Y.Korniyenko,
L.Tong,
P.Bayer,
P.Janning,
L.S.Thomashow,
D.V.Mavrodi.
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Ref.
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Proc Natl Acad Sci U S A, 2004,
101,
16431-16436.
[DOI no: ]
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PubMed id
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Abstract
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Phenazines produced by Pseudomonas and Streptomyces spp. are heterocyclic
nitrogen-containing metabolites with antibiotic, antitumor, and antiparasitic
activity. The antibiotic properties of pyocyanin, produced by Pseudomonas
aeruginosa, were recognized in the 1890s, although this blue phenazine is now
known to be a virulence factor in human disease. Despite their biological
significance, the biosynthesis of phenazines is not fully understood. Here we
present structural and functional studies of PhzF, an enzyme essential for
phenazine synthesis in Pseudomonas spp. PhzF shares topology with
diaminopimelate epimerase DapF but lacks the same catalytic residues. The
structure of PhzF in complex with its substrate,
trans-2,3-dihydro-3-hydroxyanthranilic acid, suggests that it is an isomerase
using the conserved glutamate E45 to abstract a proton from C3 of the substrate.
The proton is returned to C1 of the substrate after rearrangement of the
double-bond system, yielding an enol that converts to the corresponding ketone.
PhzF is a dimer that may be bifunctional, providing a shielded cavity for ketone
dimerization via double Schiff-base formation to produce the phenazine scaffold.
Our proposed mechanism is supported by mass and NMR spectroscopy. The results
are discussed in the context of related structures and protein sequences of
unknown biochemical function.
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Figure 1.
Fig. 1. Biosynthesis of PCA from chorismic acid via DHHA.
Also shown is the proposed mechanism of action of PhzF.
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Figure 2.
Fig. 2. Ribbon diagrams of PhzF in the open and closed
forms, substrate binding to the active site, and comparison to
the active sites of related proteins. Overall structure of PhzF
in the open (A) and closed (B) forms. Binding partners are
sulfate (A) and 3OHAA (B). Key building blocks of the C-terminal
domain in one monomer are color-coded: green, central  -helix;
blue, eight-stranded  -barrel; and red,
decorating -helices. Secondary
structure is labeled in the other monomer. The surface in B
demonstrates the size of the intermonomer cavity in the closed
form. (C) Stereoview of DHHA binding to the active site of PhzF.
The proposed position of E45 in reprotonation is shown in red.
Conserved residues are shown in magenta, and the positions of
the catalytic cysteines in DapF are shown in cyan. (D) Active
sites of DapF (Left), YddE (Center), and phenazine-biosynthesis
protein from Enterococcus faecalis V583 (Right). All structures
were prepared with BOBSCRIPT (32).
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