Structure and Function of the LmbE-like Superfamily

Abstract

The LmbE-like superfamily is comprised of a series of enzymes that use a single catalytic metal ion to catalyze the hydrolysis of various substrates. These substrates are often key metabolites for eukaryotes and prokaryotes, which makes the LmbE-like enzymes important targets for drug development. Herein we review the structure and function of the LmbE-like proteins identified to date. While this is the newest superfamily of metallohydrolases, a growing number of functionally interesting proteins from this superfamily have been characterized. Available crystal structures of LmbE-like proteins reveal a Rossmann fold similar to lactate dehydrogenase, which represented a novel fold for (zinc) metallohydrolases at the time the initial structure was solved. The structural diversity of the N-acetylglucosamine containing substrates affords functional diversity for the LmbE-like enzyme superfamily. The majority of enzymes identified to date are metal-dependent deacetylases that catalyze the hydrolysis of a N-acetylglucosamine moiety on substrate using a combination of amino acid side chains and a single bound metal ion, predominantly zinc. The catalytic zinc is coordinated to proteins via His2-Asp-solvent binding site. Additionally, studies indicate that protein dynamics play important roles in regulating access to the active site and facilitating catalysis for at least two members of this protein superfamily.

GlcNAc De- N -Acetylase from the Hyperthermophilic Archaeon Sulfolobus solfataricus

“…This was previously observed also for the de-N-acetylase from Trypanosoma brucei that was active on both GlcNAc-␣and GlcNAc-␤-PI (39). SSO2901 shows sequence similarity to a putative N-acetylglucosaminyl-phosphatidylinositol (GlcNAc-PI) de-N-acetylase from Sulfolobus islandicus belonging to the LmbE-like superfamily, which includes metal-dependent enzymes (40). All LmbE-like superfamily members possess the conserved His-X-Asp-Asp sequence (40), where the catalytic Zn 2ϩ ion in the active site is pentacoordinated by the imidazolium side chain of His.…”

“…It has been reported that mononuclear zinc enzymes are inhibited by EDTA and Zn 2ϩ (40,42), as demonstrated for the rat GlcNAc-PI de-N-acetylase (43), for BC1534 and BC3461 from B. cereus (44), and for the de-Nacetylase LpxC from E. coli (45). rSSO2901 shows the conserved His-X-Asp-Asp motif, like the LmbE-like superfamily members (40) (Fig. S7), and it is partially inactivated by EDTA and Zn 2ϩ , suggesting the presence of a catalytic metal ion in the active site of the enzyme.…”

“…The positively charged Zn 2ϩ plays an essential role in stabilizing the reaction intermediate during catalysis (41). It has been reported that mononuclear zinc enzymes are inhibited by EDTA and Zn 2ϩ (40,42), as demonstrated for the rat GlcNAc-PI de-N-acetylase (43), for BC1534 and BC3461 from B. cereus (44), and for the de-Nacetylase LpxC from E. coli (45). rSSO2901 shows the conserved His-X-Asp-Asp motif, like the LmbE-like superfamily members (40) (Fig.…”

“…SSO2901 shows sequence similarity to a putative N-acetylglucosaminyl-phosphatidylinositol (GlcNAc-PI) de-N-acetylase from Sulfolobus islandicus belonging to the LmbE-like superfamily, which includes metal-dependent enzymes (40). All LmbE-like superfamily members possess the conserved His-X-Asp-Asp sequence (40), where the catalytic Zn 2ϩ ion in the active site is pentacoordinated by the imidazolium side chain of His. The positively charged Zn 2ϩ plays an essential role in stabilizing the reaction intermediate during catalysis (41).…”

Investigation of the identity of the nucleophile initiating the hydrolysis of phosphate esters catalyzed by dinuclear mimics of metallohydrolases

“…We, and others, have explored extensively the functional roles model complexes can play in reproducing the electronic, structural and reactivity characteristics of organophosphatehydrolyzing metalloenzyme systems [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26]. One of the prominent issues targeted in these studies is the identity of the nucleophilic agent(s) in the models and in the corresponding metalloenzymes [27].…”