Crystal structure of a ternary complex of d -2-hydroxyisocaproate dehydrogenase from Lactobacillus casei , NAD + and 2-oxoisocaproate at 1.9 Å resolution 1 1Edited by R. Huber

Distinct Conformation-mediated Functions of an Active Site Loop in the Catalytic Reactions of NAD-dependent D-Lactate Dehydrogenase and Formate Dehydrogenase

“…The results obtained were clearly consistent with the roles of these active site loops that were previously proposed on the basis of structural analysis (13,14,22,23). In the case of D-LDH, the main chain amide groups of the loop seem to stabilize the binding of a substrate in the proper orientation for the catalytic action of D-LDH through interactions with the carboxyl oxygens of the substrate, in analogy to the role played by the side chain of Arg 171 in L-LDH (Fig.…”

“…2B). In the Lactobacillus casei D-HicDH structure, probably the closest approximation of a true ternary complex determined among these dehydrogenases to date (14), Val 78 and Gly 79 (Val 77 and Gly 78 in this enzyme, respectively) form hydrogen bonds with the carboxyl group of 2-ketoacid substrate (Fig. 2C).…”

“…On the other hand, the substrate-binding site of D-LDH contains only one Arg residue, Arg 235 , which possibly fulfills the roles of both Arg 109 and Arg 171 (7,8,13). The three-dimensional structure implies that the role of Arg 235 as Arg 171 may be supplemented by the main chain amide groups of Gly 78 and Val 79 on a loop structure in the active site, which act as bidentate hydrogen bond donors to the substrate carboxyl group (13,14) (Fig. 1B).…”

“…D-LDH is a member of the D-2-hydroxy-acid dehydrogenase superfamily together with glycerate (15), phosphoglycerate (16 -18), and hydroxyisocaproate dehydrogenases (14,19) and vancomycin-resistant protein H (VanH) (20). In addition, D-LDH structurally resembles NAD-dependent formate dehydrogenase (FDH, EC 1.2.1.2) (21-23) and L-alanine dehydrogenase (24), despite having less than 20% sequence similarity to these enzymes.…”

Crystallization and preliminary X-ray analysis ofD-2-hydroxyacid dehydrogenase fromHaloferax mediterranei

“…The majority of the enzymes are homodimers (Goldberg et al, 1994;Razeto et al, 2002;M. Sugahara & N. Kunishima, unpublished work), but there is some variation in their quaternary structure, with d-2-hydroxyisocaproate dehydrogenase, for example, being a homohexamer (Dengler et al, 1997). However, this hexamer is constructed from a trimer of dimers in D3 symmetry, with the dimer being the same as that of the other family members.…”