2QJN

Crystal structure of D-mannonate dehydratase from Novosphingobium aromaticivorans complexed with Mg and 2-keto-3-deoxy-D-gluconate

Summary for 2QJN

• Entry DOI: 10.2210/pdb2qjn/pdb
• Related: 2QJJ 2QJM
• Descriptor: Mandelate racemase/muconate lactonizing enzyme, MAGNESIUM ION, 2-KETO-3-DEOXYGLUCONATE, ... (4 entities in total)
• Functional Keywords: d-mannonate dehydratase, enolase superfamily, lyase
• Biological source: Novosphingobium aromaticivorans
• Total number of polymer chains: 4
• Total formula weight: 181999.42

Authors

Fedorov, A.A.,Fedorov, E.V.,Rakus, J.F.,Vick, J.E.,Gerlt, J.A.,Almo, S.C. (deposition date: 2007-07-08, release date: 2007-10-30, Last modification date: 2023-08-30)

Primary citation

Rakus, J.F.,Fedorov, A.A.,Fedorov, E.V.,Glasner, M.E.,Vick, J.E.,Babbitt, P.C.,Almo, S.C.,Gerlt, J.A.
Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans.
Biochemistry, 46:12896-12908, 2007

PubMed Abstract: 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.

PubMed: 17944491
DOI: 10.1021/bi701703w

Experimental method

X-RAY DIFFRACTION (2 Å)