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PDBsum entry 6u1v
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Oxidoreductase
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PDB id
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6u1v
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References listed in PDB file
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Key reference
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Title
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Structural mechanism of regioselectivity in an unusual bacterial acyl-Coa dehydrogenase.
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Authors
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J.M.Blake-Hedges,
J.H.Pereira,
P.Cruz-Morales,
M.G.Thompson,
J.F.Barajas,
J.Chen,
R.N.Krishna,
L.J.G.Chan,
D.Nimlos,
C.Alonso-Martinez,
E.E.K.Baidoo,
Y.Chen,
J.W.Gin,
L.Katz,
C.J.Petzold,
P.D.Adams,
J.D.Keasling.
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Ref.
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J Am Chem Soc, 2020,
142,
835-846.
[DOI no: ]
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PubMed id
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Abstract
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Terminal alkenes are easily derivatized, making them desirable functional group
targets for polyketide synthase (PKS) engineering. However, they are rarely
encountered in natural PKS systems. One mechanism for terminal alkene formation
in PKSs is through the activity of an acyl-CoA dehydrogenase (ACAD). Herein, we
use biochemical and structural analysis to understand the mechanism of terminal
alkene formation catalyzed by an γ,δ-ACAD from the biosynthesis of the
polyketide natural product FK506, TcsD. While TcsD is homologous to canonical
α,β-ACADs, it acts regioselectively at the γ,δ-position and only on
α,β-unsaturated substrates. Furthermore, this regioselectivity is controlled
by a combination of bulky residues in the active site and a lateral shift in the
positioning of the FAD cofactor within the enzyme. Substrate modeling suggests
that TcsD utilizes a novel set of hydrogen bond donors for substrate activation
and positioning, preventing dehydrogenation at the α,β position of substrates.
From the structural and biochemical characterization of TcsD, key residues that
contribute to regioselectivity and are unique to the protein family were
determined and used to identify other putative γ,δ-ACADs that belong to
diverse natural product biosynthetic gene clusters. These predictions are
supported by the demonstration that a phylogenetically distant homologue of TcsD
also regioselectively oxidizes α,β-unsaturated substrates. This work
exemplifies a powerful approach to understand unique enzymatic reactions and
will facilitate future enzyme discovery, inform enzyme engineering, and aid
natural product characterization efforts.
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Secondary reference #1
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Title
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Towards automated crystallographic structure refinement with phenix.Refine.
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Authors
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P.V.Afonine,
R.W.Grosse-Kunstleve,
N.Echols,
J.J.Headd,
N.W.Moriarty,
M.Mustyakimov,
T.C.Terwilliger,
A.Urzhumtsev,
P.H.Zwart,
P.D.Adams.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2012,
68,
352-367.
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PubMed id
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Secondary reference #2
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Title
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Phenix: a comprehensive python-Based system for macromolecular structure solution.
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Authors
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P.D.Adams,
P.V.Afonine,
G.Bunkóczi,
V.B.Chen,
I.W.Davis,
N.Echols,
J.J.Headd,
L.W.Hung,
G.J.Kapral,
R.W.Grosse-Kunstleve,
A.J.Mccoy,
N.W.Moriarty,
R.Oeffner,
R.J.Read,
D.C.Richardson,
J.S.Richardson,
T.C.Terwilliger,
P.H.Zwart.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2010,
66,
213-221.
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PubMed id
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