This is the first crystallographic indication of the 'base-on' mode of cobalamin binding. An unusually long cobalt-base bond seems to favor homolytic cleavage of the cobalt-carbon bond and therefore to favor radical enzyme catalysis. Reactive radical intermediates can be protected from side reactions by spatial isolation inside the barrel. On the basis of unique direct interactions between the potassium ion and the two hydroxyl groups of the substrate, direct participation of a potassium ion in enzyme catalysis is strongly suggested.

Recombinant glycerol dehydratase of Klebsiella pneumoniae was purified to homogeneity. The subunit composition of the enzyme was most probably a 2 b 2 c 2 . When (R)-and (S)-propane-1,2-diols were used independently as substrates, the rate with the (R)-enantiomer was 2.5 times faster than that with the (S)-isomer. In contrast to diol dehydratase, an isofunctional enzyme, the affinity of the enzyme for the (S)-isomer was essentially the same or only slightly higher than that for the (R)-isomer (K m(R) /K m(S) ¼ 1.5). The crystal structure of glycerol dehydratase in complex with cyanocobalamin and propane-1,2-diol was determined at 2.1 Å resolution. The enzyme exists as a dimer of the abc heterotrimer. Cobalamin is bound at the interface between the a and b subunits in the so-called Ôbase-onÕ mode with 5,6-dimethylbenzimidazole of the nucleotide moiety coordinating to the cobalt atom. The electron density of the cyano group was almost unobservable, suggesting that the cyanocobalamin was reduced to cob(II)alamin by X-ray irradiation. The active site is in a (b/a) 8 barrel that was formed by a central region of the a subunit. The substrate propane-1,2-diol and essential cofactor K + are bound inside the (b/a) 8 barrel above the corrin ring of cobalamin. K + is heptacoordinated by the two hydroxyls of the substrate and five oxygen atoms from the active-site residues. These structural features are quite similar to those of diol dehydratase. A closer contact between the a and b subunits in glycerol dehydratase may be reminiscent of the higher affinity of the enzyme for adenosylcobalamin than that of diol dehydratase. Although racemic propane-1,2-diol was used for crystallization, the substrate bound to glycerol dehydratase was assigned to the (R)-isomer. This is in clear contrast to diol dehydratase and accounts for the difference between the two enzymes in the susceptibility of suicide inactivation by glycerol.Keywords: coenzyme B 12 ; adenosylcobalamin; glycerol dehydratase; crystal structure; radical enzyme catalysis.Adenosylcobalamin is one of the most unique compounds in nature. It is a water-soluble organometallic compound possessing a Co-C r bond and serves as a cofactor for enzymatic radical reactions including carbon skeleton rearrangements, heteroatom eliminations and intramolecular amino group migrations [1]. Diol dehydratase (EC 4.2.1.28) of Klebsiella oxytoca is an adenosylcobalamin (AdoCbl 1 ) dependent enzyme that catalyzes the conversions of 1,2-diols, such as propane-1,2-diol, glycerol, and 1,2-ethanediol, to the corresponding aldehydes [2,3] (Fig. 1). This enzyme has been studied intensively to establish the mechanism of action of AdoCbl [4][5][6][7]. The structurefunction relationship of the coenzyme has also been investigated extensively with this enzyme [5][6][7][8]. Recently, we have reported the three-dimensional structures of its complexes with cyanocobalamin [9] and adeninylpentylcobalamin [10] and theoretical calculations of the entire energy profile along the reaction pathway with a simplifie...

Eubacterial leucyl/phenylalanyl-tRNA protein transferase (LF-transferase) catalyses peptide-bond formation by using Leu-tRNA(Leu) (or Phe-tRNA(Phe)) and an amino-terminal Arg (or Lys) of a protein, as donor and acceptor substrates, respectively. However, the catalytic mechanism of peptide-bond formation by LF-transferase remained obscure. Here we determine the structures of complexes of LF-transferase and phenylalanyl adenosine, with and without a short peptide bearing an N-terminal Arg. Combining the two separate structures into one structure as well as mutation studies reveal the mechanism for peptide-bond formation by LF-transferase. The electron relay from Asp 186 to Gln 188 helps Gln 188 to attract a proton from the alpha-amino group of the N-terminal Arg of the acceptor peptide. This generates the attacking nucleophile for the carbonyl carbon of the aminoacyl bond of the aminoacyl-tRNA, thus facilitating peptide-bond formation. The protein-based mechanism for peptide-bond formation by LF-transferase is similar to the reverse reaction of the acylation step observed in the peptide hydrolysis reaction by serine proteases.

Eubacterial leucyl/phenylalanyl‐tRNA protein transferase (L/F‐transferase), encoded by the aat gene, conjugates leucine or phenylalanine to the N‐terminal Arg or Lys residue of proteins, using Leu‐tRNALeu or Phe‐tRNAPhe as a substrate. The resulting N‐terminal Leu or Phe acts as a degradation signal for the ClpS‐ClpAP‐mediated N‐end rule protein degradation pathway. Here, we present the crystal structures of Escherichia coli L/F‐transferase and its complex with an aminoacyl‐tRNA analog, puromycin. The C‐terminal domain of L/F‐transferase consists of the GCN5‐related N‐acetyltransferase fold, commonly observed in the acetyltransferase superfamily. The p‐methoxybenzyl group of puromycin, corresponding to the side chain of Leu or Phe of Leu‐tRNALeu or Phe‐tRNAPhe, is accommodated in a highly hydrophobic pocket, with a shape and size suitable for hydrophobic amino‐acid residues lacking a branched β‐carbon, such as leucine and phenylalanine. Structure‐based mutagenesis of L/F‐transferase revealed its substrate specificity. Furthermore, we present a model of the L/F‐transferase complex with tRNA and substrate proteins bearing an N‐terminal Arg or Lys.

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