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PDBsum entry 2ccc
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References listed in PDB file
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Key reference
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Title
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Dodecins: a family of lumichrome binding proteins.
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Authors
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M.Grininger,
K.Zeth,
D.Oesterhelt.
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Ref.
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J Mol Biol, 2006,
357,
842-857.
[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
perfect match.
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Abstract
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Dodecin is a small dodecameric flavoprotein from Halobacterium salinarum that
contains two flavins stacked between two tryptophan residues to form an aromatic
tetrade. The functional properties of heterologously expressed dodecin were
investigated by fluorescence spectroscopy, which allowed the determination of
dissociation constants for a number of protein-ligand complexes. The values
obtained were in the nanomolar to micromolar range and correlate positively with
the ligand size. These data were supplemented by X-ray crystal structures of the
apododecin and holocomplexes with lumichrome, lumiflavin, riboflavin and FMN at
resolutions between 1.55 to 1.95A to unravel a gating mechanism as the
structural basis for the preferential binding of the small ligands lumichrome
and lumiflavin. The detailed analysis of the dodecin manifold for preferential
binding of lumichrome and lumiflavin provides insight on a subatom level into a
protein's strategy to gain selectivity for low molecular mass compounds by
steric restrictions rather than specific interactions. Investigations on the
ligand composition of a wild-type dodecin crystal (1.32A resolution) support
conclusions of functional and structural investigations on heterologously
expressed dodecin, and strongly suggest that lumichrome, a molecule associated
with the flavin metabolism, is a ligand of dodecin in vivo. Studies on mutant
protein and a Halorhodospira halophila homologue spread the idea of a lumichrome
binding system as a possible "waste"-trapping device, widely
distributed in prokaryotes.
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Figure 1.
Figure 1. The riboflavin holocomplex. Surface
representation of dodecin with the section through the
holocomplex along a C2 axis uncovers the dodecin binding pocket.
H-bonds are represented by red dotted lines. The residues (Trp36
and Gln55) mediate binding of the isoalloxazine ring; H-bonds
between Glu45 and the ribityl chain (O2' and O3') as well as
Val35 and O2' direct the aliphatic moiety towards the outer
surface. Due to an intramolecular interaction (O4'-N1), the
ribityl chain conformation is stabilized up to the O4' atom.
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Figure 3.
Figure 3. Overall structure of H. salinarum dodecin. (a)
View along the 3-fold axis. The monomer is highlighted through
its corresponding molecular surface. Monomers of a trimer are
held in red, green and blue, the ligand (riboflavin) is colored
in gold. Heteroatoms of residues important for binding as well
as of the ligand are colored red (O) and blue (N). b2-Strands of
the monomers mediate the contacts in the trimer extending to a
five-stranded antiparallel b-sheet. Four trimers are arranged in
a dodecamer of 23-cubic symmetry. (b) and (c) View on the
arrangement of two trimers along the 2-fold axis. In (b) one
trimer is highlighted through its corresponding molecular
surface. In the riboflavin holocomplex (H-RBF) a dimer of
riboflavin is embedded between the indole groups of tryptophan
(Trp36) with their ribityl chain pointing towards the outer
surface. Monomers of a dodecameric assembly are marked by
superscript alphabetic characters.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2006,
357,
842-857)
copyright 2006.
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