The folding and quaternary structure of trimeric 2-keto-3-deoxy-6-phosphogluconic aldolase at 3.5- Å resolution

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Abstract
An X-ray crystallographic structure determination was carried out on 2-keto-3-deoxy-6-phosphogluconic (KDPG) aldolase at 3.5 .ANG. resolution using the multiple isomorphous replacement method with 3 heavy atom derivatives along with anomalous dispersion contributions from 2 of the derivatives. Crystals grown from ammonium sulfate-phosphate buffered (pH 3.5) solutions were cubic, a = 103.40 (4) .ANG., space group P213. KDPG aldolase consists of trimeric heterologous assemblages utilizing crystallographic 3-fold symmetry. The overall profile of the oligomeric structure viewed down the 3-fold axis resembles that of a ship propeller while the subunits are approximate irregular oblate ellipsoids (25 .times. 45 .times. 45 .ANG.). The folding of most of the polypeptide chain was traced unambiguously. Secondary structural features consist of 9 helical regions (75 residues, 35%) and a pair of 2 parallel chains. The subunit contains a long empty channel which is about 9 .times. 9 .times. 30 .ANG. with 1 of the pair of parallel chains forming part of the wall. Three Hg binding sites are located in this channel. These might correspond to the 2 readily accessible and 1 of the 2 buried cysteine residues of each subunit. The channel terminates with another cavity of .apprx. 8 .times. 10 .times. 25 .ANG. near the surface of the oligomeric structure. The regions of the subunits near the 3-fold axis are characterized by a high degree of secondary structural organization and these make close intersubunit contacts. Quaternary interactions are due mainly to side-chain interactions of helices.