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PDBsum entry 4mnc
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Transport protein
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PDB id
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4mnc
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References listed in PDB file
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Key reference
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Title
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Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
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Authors
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M.W.Vetting,
N.Al-Obaidi,
S.Zhao,
B.San francisco,
J.Kim,
D.J.Wichelecki,
J.T.Bouvier,
J.O.Solbiati,
H.Vu,
X.Zhang,
D.A.Rodionov,
J.D.Love,
B.S.Hillerich,
R.D.Seidel,
R.J.Quinn,
A.L.Osterman,
J.E.Cronan,
M.P.Jacobson,
J.A.Gerlt,
S.C.Almo.
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Ref.
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Biochemistry, 2015,
54,
909-931.
[DOI no: ]
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PubMed id
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Abstract
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The rate at which genome sequencing data is accruing demands enhanced methods
for functional annotation and metabolism discovery. Solute binding proteins
(SBPs) facilitate the transport of the first reactant in a metabolic pathway,
thereby constraining the regions of chemical space and the chemistries that must
be considered for pathway reconstruction. We describe high-throughput protein
production and differential scanning fluorimetry platforms, which enabled the
screening of 158 SBPs against a 189 component library specifically tailored for
this class of proteins. Like all screening efforts, this approach is limited by
the practical constraints imposed by construction of the library, i.e., we can
study only those metabolites that are known to exist and which can be made in
sufficient quantities for experimentation. To move beyond these inherent
limitations, we illustrate the promise of crystallographic- and mass
spectrometric-based approaches for the unbiased use of entire metabolomes as
screening libraries. Together, our approaches identified 40 new SBP ligands,
generated experiment-based annotations for 2084 SBPs in 71 isofunctional
clusters, and defined numerous metabolic pathways, including novel catabolic
pathways for the utilization of ethanolamine as sole nitrogen source and the use
of d-Ala-d-Ala as sole carbon source. These efforts begin to define an
integrated strategy for realizing the full value of amassing genome sequence
data.
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