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PDBsum entry 1gxo
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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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Convergent evolution sheds light on the anti-Beta -Elimination mechanism common to family 1 and 10 polysaccharide lyases.
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Authors
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S.J.Charnock,
I.E.Brown,
J.P.Turkenburg,
G.W.Black,
G.J.Davies.
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Ref.
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Proc Natl Acad Sci U S A, 2002,
99,
12067-12072.
[DOI no: ]
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PubMed id
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Abstract
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Enzyme-catalyzed beta-elimination of sugar uronic acids, exemplified by the
degradation of plant cell wall pectins, plays an important role in a wide
spectrum of biological processes ranging from the recycling of plant biomass
through to pathogen virulence. The three-dimensional crystal structure of the
catalytic module of a "family PL-10" polysaccharide lyase, Pel10Acm
from Cellvibrio japonicus, solved at a resolution of 1.3 A, reveals a new
polysaccharide lyase fold and is the first example of a polygalacturonic acid
lyase that does not exhibit the "parallel beta-helix" topology. The
"Michaelis" complex of an inactive mutant in association with the
substrate trigalacturonate/Ca2+ reveals the catalytic machinery harnessed by
this polygalacturonate lyase, which displays a stunning resemblance, presumably
through convergent evolution, to the tetragalacturonic acid complex observed for
a structurally unrelated polygalacturonate lyase from family PL-1. Common
coordination of the -1 and +1 subsite saccharide carboxylate groups by a
protein-liganded Ca2+ ion, the positioning of an arginine catalytic base in
close proximity to the alpha-carbon hydrogen and numerous other conserved
enzyme-substrate interactions, considered in light of mutagenesis data for both
families, suggest a generic polysaccharide anti-beta-elimination mechanism.
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Figure 3.
Fig 3. Schematic diagram of the interactions of the mutant
D389A Pel10Acm with trigalacturonate. The approximate location
of Asp389 from the native structure is indicated for reference.
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Figure 4.
Fig 4. (a) More O'Ferral diagram for  -elimination of
galacto-configured uronic acids. (b) Putative E1cb/asynchronous
E2 reaction mechanism for Pel10 and related enzymes in which
proton abstraction by arginine is followed by leaving-group
elimination. The essential role of Asp389 may involve a role in
binding a second Ca^2+ ion as observed in Pel1C.
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