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PDBsum entry 1d8c
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structure of escherichia coli malate synthase g complexed with magnesium and glyoxylate at 2.0 a resolution: mechanistic implications.
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Authors
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B.R.Howard,
J.A.Endrizzi,
S.J.Remington.
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Ref.
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Biochemistry, 2000,
39,
3156-3168.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of selenomethionine-substituted malate synthase G, an 81
kDa monomeric enzyme from Escherichia coli has been determined by MAD phasing,
model building, and crystallographic refinement to a resolution of 2.0 A. The
crystallographic R factor is 0.177 for 49 242 reflections observed at the
incident wavelength of 1.008 A, and the model stereochemistry is satisfactory.
The basic fold of the enzyme is that of a beta8/alpha8 (TIM) barrel. The barrel
is centrally located, with an N-terminal alpha-helical domain flanking one side.
An inserted beta-sheet domain folds against the opposite side of the barrel, and
an alpha-helical C-terminal domain forms a plug which caps the active site.
Malate synthase catalyzes the condensation of glyoxylate and acetyl-coenzyme A
and hydrolysis of the intermediate to yield malate and coenzyme A, requiring
Mg(2+). The structure reveals an enzyme-substrate complex with glyoxylate and
Mg(2+) which coordinates the aldehyde and carboxylate functions of the
substrate. Two strictly conserved residues, Asp631 and Arg338, are proposed to
provide concerted acid-base chemistry for the generation of the enol(ate)
intermediate of acetyl-coenzyme A, while main-chain hydrogen bonds and bound
Mg(2+) polarize glyoxylate in preparation for nucleophilic attack. The catalytic
strategy of malate synthase appears to be essentially the same as that of
citrate synthase, with the electrophile activated for nucleophilic attack by
nearby positive charges and hydrogen bonds, while concerted acid-base catalysis
accomplishes the abstraction of a proton from the methyl group of
acetyl-coenzyme A. An active site aspartate is, however, the only common feature
of these two enzymes, and the active sites of these enzymes are produced by
quite different protein folds. Interesting similarities in the overall folds and
modes of substrate recognition are discussed in comparisons of malate synthase
with pyruvate kinase and pyruvate phosphate dikinase.
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