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PDBsum entry 4z0p
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Oxidoreductase
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PDB id
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4z0p
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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, Biochemical, And evolutionary characterizations of glyoxylate/hydroxypyruvate reductases show their division into two distinct subfamilies.
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Authors
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J.Kutner,
I.G.Shabalin,
D.Matelska,
K.B.Handing,
O.Gasiorowska,
P.Sroka,
M.W.Gorna,
K.Ginalski,
K.Wozniak,
W.Minor.
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Ref.
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Biochemistry, 2018,
57,
963-977.
[DOI no: ]
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PubMed id
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Abstract
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The d-2-hydroxyacid dehydrogenase (2HADH) family illustrates a complex
evolutionary history with multiple lateral gene transfers and gene duplications
and losses. As a result, the exact functional annotation of individual members
can be extrapolated to a very limited extent. Here, we revise the previous
simplified view on the classification of the 2HADH family; specifically, we show
that the previously delineated glyoxylate/hydroxypyruvate reductase (GHPR)
subfamily consists of two evolutionary separated GHRA and GHRB subfamilies. We
compare two representatives of these subfamilies from Sinorhizobium meliloti
(SmGhrA and SmGhrB), employing a combination of biochemical, structural, and
bioinformatics approaches. Our kinetic results show that both enzymes reduce
several 2-ketocarboxylic acids with overlapping, but not equivalent, substrate
preferences. SmGhrA and SmGhrB show highest activity with glyoxylate and
hydroxypyruvate, respectively; in addition, only SmGhrB reduces
2-keto-d-gluconate, and only SmGhrA reduces pyruvate (with low efficiency). We
present nine crystal structures of both enzymes in apo forms and in complexes
with cofactors and substrates/substrate analogues. In particular, we determined
a crystal structure of SmGhrB with 2-keto-d-gluconate, which is the biggest
substrate cocrystallized with a 2HADH member. The structures reveal significant
differences between SmGhrA and SmGhrB, both in the overall structure and within
the substrate-binding pocket, offering insight into the molecular basis for the
observed substrate preferences and subfamily differences. In addition, we
provide an overview of all GHRA and GHRB structures complexed with a ligand in
the active site.
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