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PDBsum entry 2isl
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References listed in PDB file
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Key reference
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Title
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Blub cannibalizes flavin to form the lower ligand of vitamin b12.
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Authors
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M.E.Taga,
N.A.Larsen,
A.R.Howard-Jones,
C.T.Walsh,
G.C.Walker.
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Ref.
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Nature, 2007,
446,
449-453.
[DOI no: ]
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PubMed id
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Abstract
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Vitamin B12 (cobalamin) is among the largest known non-polymeric natural
products, and the only vitamin synthesized exclusively by microorganisms. The
biosynthesis of the lower ligand of vitamin B(12), 5,6-dimethylbenzimidazole
(DMB), is poorly understood. Recently, we discovered that a Sinorhizobium
meliloti gene, bluB, is necessary for DMB biosynthesis. Here we show that BluB
triggers the unprecedented fragmentation and contraction of the bound flavin
mononucleotide cofactor and cleavage of the ribityl tail to form DMB and
D-erythrose 4-phosphate. Our structural analysis shows that BluB resembles an
NAD(P)H-flavin oxidoreductase, except that its unusually tight binding pocket
accommodates flavin mononucleotide but not NAD(P)H. We characterize
crystallographically an early intermediate along the reaction coordinate,
revealing molecular oxygen poised over reduced flavin. Thus, BluB isolates and
directs reduced flavin to activate molecular oxygen for its own cannibalization.
This investigation of the biosynthesis of DMB provides clarification of an
aspect of vitamin B12 that was otherwise incomplete, and may contribute to a
better understanding of vitamin B12-related disease.
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Figure 2.
Figure 2: Structure of BluB. a, Ribbon diagram of BluB
with FMN in the binding pocket (stick representation). The
two-fold axis is perpendicular to the plane of the figure. b, E.
coli nitroreductase NfsB (Protein Data Bank 1ICR)^21 with FMN
and nicotinic acid (stick representation) in the binding pocket.
c, Cross-section of BluB's molecular surface. The two-fold axis
lies along the y axis such that the si-face of FMN is viewed on
the left and re-face on the right. The surface is coloured
according to electrostatic potential, where blue is
electropositive, red is electronegative and k[B] is Boltzmann's
constant. The back and front of the surface are cut away to
reveal the FMN binding pocket buried in the dimer interface. The
pocket wraps snugly around FMN, preventing interaction with
other substrates. d, The BluB ribbon diagram has been coloured
according to B-factor. Red represents flexible regions that may
control or gate access to the active site.
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Figure 3.
Figure 3: Active site of BluB. a, b, The active site with
oxidized FMN (a) and reduced FMN (b), viewed from the re-face.
H-bonds are represented as dashed lines. For clarity, water
molecules are not rendered in this view. The rearrangement in
H-bonds around N1 reflects the change in protonation in the
reduced structure. Asp 32 may also form a close contact with C1'
of the ribityl chain, suggesting a potential catalytic role for
this residue. c, d, Side views of the active site in the
oxidized (c) and reduced (d) structures. For clarity, Arg 34 has
not been rendered in this view. The sigma-A weighted 2F[o]-F[c]
electron density map is contoured at 1  and
coloured grey (around protein side chains), blue (around
FMN/FMNH[2]) and red (around water/oxygen) to enhance contrast.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2007,
446,
449-453)
copyright 2007.
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Secondary reference #1
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Title
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Sinorhizobium meliloti blub is necessary for production of 5,6-Dimethylbenzimidazole, The lower ligand of b12.
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Authors
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G.R.Campbell,
M.E.Taga,
K.Mistry,
J.Lloret,
P.J.Anderson,
J.R.Roth,
G.C.Walker.
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Ref.
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Proc Natl Acad Sci U S A, 2006,
103,
4634-4639.
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PubMed id
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