2qjm
From Proteopedia
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Crystal structure of the K271E mutant of Mannonate dehydratase from Novosphingobium aromaticivorans complexed with Mg and D-mannonate
Overview
The d-mannonate dehydratase (ManD) function was assigned to a group of, orthologous proteins in the mechanistically diverse enolase superfamily by, screening a library of acid sugars. Structures of the wild type ManD from, Novosphingobium aromaticivorans were determined at pH 7.5 in the presence, of Mg2+ and also in the presence of Mg2+ and the 2-keto-3-keto-d-gluconate, dehydration product; the structure of the catalytically active K271E, mutant was determined at pH 5.5 in the presence of the d-mannonate, substrate. As previously observed in the structures of other members of, the enolase superfamily, ManD contains two domains, an N-terminal, alpha+beta capping domain and a (beta/alpha)7beta-barrel domain. The, barrel domain contains the ligands for the essential Mg2+, Asp 210, Glu, 236, and Glu 262, at the ends of the third, fourth, and fifth beta-strands, of the barrel domain, respectively. However, the barrel domain lacks both, the Lys acid/base catalyst at the end of the second beta-strand and the, His-Asp dyad acid/base catalyst at the ends of the seventh and sixth, beta-strands, respectively, that are found in many members of the, superfamily. Instead, a hydrogen-bonded dyad of Tyr 159 in a loop, following the second beta-strand and Arg 147 at the end of the second, beta-strand are positioned to initiate the reaction by abstraction of the, 2-proton. Both Tyr 159 and His 212, at the end of the third beta-strand, are positioned to facilitate both syn-dehydration and ketonization of the, resulting enol intermediate to yield the 2-keto-3-keto-d-gluconate product, with the observed retention of configuration. The identities and locations, of these acid/base catalysts as well as of cationic amino acid residues, that stabilize the enolate anion intermediate define a new structural, strategy for catalysis (subgroup) in the mechanistically diverse enolase, superfamily. With these differences, we provide additional evidence that, the ligands for the essential Mg2+ are the only conserved residues in the, enolase superfamily, establishing the primary functional importance of the, Mg2+-assisted strategy for stabilizing the enolate anion intermediate.
About this Structure
2QJM is a Single protein structure of sequence from Novosphingobium aromaticivorans with and as ligands. Full crystallographic information is available from OCA.
Reference
Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans., Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Vick JE, Babbitt PC, Almo SC, Gerlt JA, Biochemistry. 2007 Nov 13;46(45):12896-908. Epub 2007 Oct 18. PMID:17944491
Page seeded by OCA on Wed Jan 23 11:03:00 2008
